Zebrafish transcriptome sequencing project
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ABSTRACT:
REPOSITORIES: ENA
Similar Datasets
Project description:Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer
| PRJEB1986 | ENA
Project description:Proteome Sequencing of zebrafish brain after nanoplastics exposure
2024-11-01 | PXD057416 |
Project description:Total RNA was extracted from zebrafish embryos collected for one or more alleles identified by the Zebrafish Mutation Project (http://www.sanger.ac.uk/Projects/D_rerio/zmp/). The mRNA was pulled down using polyT oligos attached to magnetic beads and Illumina libraries were prepared using TruSeq Stranded mRNA SamplePreparation Kits (RS-122-2101 and RS-122-2102) according to manufacturer's instructions. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2015-01-08 | E-ERAD-326 | biostudies-arrayexpress
Project description:Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. Recent years have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes, yet large gaps still remain in the functional pathways critical for each developmental stage, especially for the late embryonic development. We sequenced the polyA-extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish
2013-04-30 | E-GEOD-45706 | biostudies-arrayexpress
Project description:Total RNA was extracted from morpholically abnormal and sibling wild type embryos identified by the Zebrafish Mutation Project (http://www.sanger.ac.uk/Projects/D_rerio/zmp/). The 3 end of fragmented RNA was pulled down using polyToligos attached to magnetic beads, reverse transcribed, made into Illumina libraries and sequenced using Illumina HiSeq paired-end sequencing. Protocol: Total RNA was extracted from zebrafish embryos using Trizol and DNase treated. Chemically fragmented RNA was enriched for the 3 ends by pulled down using an anchored polyToligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 2 was ligated to the 5 end of the captured RNA and the RNA was eluted from the beads. Reverse transcription was primed with an anchored polyT oligo with part of Illumina adapter 1 at the 5 end followed by 12 random bases, then an 8 base indexing tags, then CG and 14 T bases. An Illumina library with full adapter sequence was produced by 20 cycles of PCR. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2014-05-27 | E-ERAD-244 | biostudies-arrayexpress
Project description:With the emergence of zebrafish as an important model organism, a concerted effort has been made to study its transcriptome. This effort is limited by gaps in zebrafish annotation, which is especially pronounced concerning transcripts dynamically expressed during zygotic genome activation (ZGA). To date, short read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome, the current annotation is rudimentary. By providing direct observation of full-length transcripts, recently refined long-read sequencing platforms can dramatically improve annotation coverage and accuracy. Here, we leveraged the SMRT platform to study the early ZGA-stage zebrafish transcriptome. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome, identifying 2748 high confidence novel transcripts that originated from previously unannotated loci and 1835 new isoforms in previously annotated genes.
2018-05-24 | GSE101843 | GEO
Project description:A Pilot Project for Zebrafish Tilling by Illumina Sequencing
| PRJEB2193 | ENA
Project description:The present study was conducted in the frame of the EU-funded Graphene Flagship project. We previously evaluated the impact of graphene oxide (GO) on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild-type versus AhR-deficient zebrafish. Here, we performed single-cell RNA-sequencing (10x Genomics) on whole (dissociated) germ-free (GF) zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.
2022-07-22 | E-MTAB-11984 | biostudies-arrayexpress
Project description:Total RNA was extracted from morpholically abnormal and sibling wild type embryos identified by the Zebrafish Mutation Project (http://www.sanger.ac.uk/Projects/D_rerio/zmp/). The 3 end of fragmented RNA was pulled down using polyToligos attached to magnetic beads, reverse transcribed, made into Illumina libraries and sequenced using IlluminaHiSeq paired-end sequencing. Protocol: Total RNA was extracted from mouse embryos using Trizol and DNase treated. Chemically fragmented RNA was enriched for the 3 ends by pulled down using an anchored polyToligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 2 was ligated to the 5 end of the captured RNA and the RNA was eluted from the beads. Reverse transcription was primed with an anchored polyToligo with part of Illumina adapter 1 at the 5 end followed by 4 random bases, then an A, C or G base, then one of twelve5 base indexing tags and 14 T bases. An Illumina library with full adapter sequence was produced by 15 cycles of PCR. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2013-02-21 | E-ERAD-91 | biostudies-arrayexpress
Project description:Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. Recent years have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes, yet large gaps still remain in the functional pathways critical for each developmental stage, especially for the late embryonic development. We sequenced the polyA-extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development.
2013-04-30 | GSE45706 | GEO