biostudies-arrayexpressAdelino CanarioDanio reriohttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15099sst6 follows Tostivint et al 2019 gene naming (doi:10.1016/j.ygcen.2019.02.022). The experiment intended to identify the main transcript differences between the zebrafish somatostatin 6 mutants and wild type at 0, 3 and 6 hours post fertilization, as well as to identify maternal and zygotic activated genes.biostudies-arrayexpressSequencing - The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.Nucleic Acid Extraction - Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)Sample Collection - recently fertilized (0), 3 and 6 hours post fertilization embros were collected into RNA laterLibrary Construction - Ribo-off rRNA Depletion Kit（vazyme, Nanjing, China）was used to remove ribosomal RNA, then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Expression level of mRNA - The known reference gene sequences and annotation files were used as database to calculate the expression abundance of the genes encoding each protein in each sample was identified by sequence similarity comparison. htseq-count (1) was used to obtain the number of reads aligned to the protein-coding gene in each sample, and calculate the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) = [RMg * 109 ] / [RMt * L] • RMg: The number of reads mapped to the gene • RMt: The total number of read mapped to protein-coding sequences in the alignment • L: The length of the gene in base pairs Expression level of lncRNA - the expression abundance of each transcript in each sample was found by sequence similarity alignment using bowtie2 (2) and eXpress (3). FPKM was calculated as above. Expression of circRNA - RPB (junction reads per billion mapped reads) was used to quantify circRNA. The RPB was calculated as follows number of circular reads / number of total reads (million) *1000 in which number of circular reads indicates the number of reads aligned to the back-spliced junctions region of circRNA, which is derived from the number of reads in the circRNA prediction software that supports circRNA ringing. Number of Total Reads (Units in Million) indicates the number of (clean_data) reads in each sample sequencing data (in million). 1 Anders S, Pyl P T, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics, 2015, 31(2):166-9. 2 Langmead B and Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature methods. 2012, 9(4):357-359. 3 Roberts A and Pachter L. Streaming fragment assignment for real-time analysis of sequencing experiments. Nature methods. 2013,10(1):71-73.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsAgilent 2100 BioanalyzerIllumina NovaSeq 6000RNA-seq of coding RNADanio rerioAdelino CanariofalseRNA-Seq of CRISPR/Cas9 zebrafish somatostatin 6 (sst6) mutant embryos at 0, 3 and 6 hours post fertilization compared to wild type controlssst6 follows Tostivint et al 2019 gene naming (doi:10.1016/j.ygcen.2019.02.022). The experiment intended to identify the main transcript differences between the zebrafish somatostatin 6 mutants and wild type at 0, 3 and 6 hours post fertilization, as well as to identify maternal and zygotic activated genes.2026-06-30T00:00:00Z2026-06-30T01:00:54.482Z2025-04-29T21:34:23.862ZE-MTAB-15099ERP172089EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184