run_metadata: 28940
This data as json
| rowid | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
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| 28940 | SRR26846105 | SRX22541614 | SRS19551199 | SRP472260 | PRJNA1040930 | Slam seq reveals that miR 430 regulates zygotic mRNA during zebrafish embryogenesis [titration data] | GSE247934 | Other | Background: Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs it has been challenging to study their expression dynamics separately. Results: By employing Slam seq a nascent mRNA labeling transcriptomic approach in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal zygotic genes emphasizing their pivotal role in early embryogenesis. We provide an hourly resolution of de novo transcriptional waves and follow nascent mRNA trajectories finding that most de novo transcriptional events are stable throughout this period. Additionally by blocking microRNA430 function a key post transcriptional regulator during zebrafish embryogenesis we directly show that it destabilizes hundreds of de novo transcribed mRNAs from pure zygotic as well as maternal zygotic genes. This unveils a novel miR 430 function during embryogenesis fine tuning zygotic gene expression which highlights that Slam seq can be used to disentangle transcriptional and post transcriptional regulation of mRNA levels. Conclusion: Such valuable insights into zebrafish early embryo transcriptome dynamics emphasize the significance of post transcriptional regulators in zygotic genome activation. These findings pave the way for future investigations into the coordinated interplay between transcriptional and post transcriptional landscapes required for the establishment of animal cell identities and functions. Overall design: Zebrafish embryos were dechorionated and either non injected or injected at single cell stage with 1000pL of 25/50/75mM s4 UTP by itself or the highest dose with 200µg/µl Alpha Amanitin. Embryos were kept in the dark until collection time shield stage 6 hours post injection. Total RNA was extracted and kept away from direct light alkylated used for library preparation with QuantSeq three prime mRNA Seq Library Prep Kit for Illumina FWD. | parent bioproject:PRJNA1040928 | pubmed:38504288 | zebrafish 7hours aamanitin 75mM s4u r3 | GSM7903289 | source name:Embryos at shield stage|tissue:Embryos|Stage:shield stage|genotype:Offspring of [AB TU]x[TL TLF]|treatment:aamanitin 75mM s4u|geo loc name:missing|collection date:missing | zebrafish 7hours aamanitin 75mM s4u r3 | Slamdunk 0.4.3. Reads that contain at least 2 T>C conversions were deemed labeled. Assembly: danRer11 Supplementary files format and content: Comma separated values <.csv>; Total raw read and labeled read counts for all experiments and samples including spike ins. Rows represent different three primeUTR isoforms for coding genes or full length transcript non coding genes. Columns represent: Ensembl gene IDs by itself non coding transcripts + three primeUTR isoforms coding transcripts or ERCC IDs spike ins; Chromosome name; Genomic start of feature; Genomic end of feature; DNA strand of feature; Number of Ts within feature; | Embryos at shield stage | Embryos were dechorionated and either non injected or injected at single cell stage with 1000pL of 25/50/75mM s4 UTP by itself or the highest dose with 200mg/mL Alpha Amanitin | Trizol™ QuantSeq 3′ mRNA‐Seq Library Prep Kit for Illumina FWD with 24 reactions Lexogen GmbH cat. no. 015.24 Lexogen i7 6 nt Index Set. | Zebrafish embryos were collected from natural breeding with random mating parents embryos were kept at 28.5 C in 0.5x Embryo Media. | tissue:Embryos|Stage:shield stage|genotype:Offspring of [AB TU]x[TL TLF]|treatment:aamanitin 75mM s4u | GSM7903289 | GSM7903289: zebrafish 7hours aamanitin 75mM s4u r3; Danio rerio; RNA Seq | GSM7903289 r1 | GSM7903289 | 1 | Trizol™ QuantSeq 3′ mRNA‐Seq Library Prep Kit for Illumina FWD with 24 reactions Lexogen GmbH cat. no. 015.24 Lexogen i7 6 nt Index Set. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP472260 | s75mM_s4U_Alpha_AM_3_7.2hpf.fastq | fastq | 2324253052.0 | 30582277.0 | GSM7903289 r1 | 0:76 | A:730230137;C:445929142;G:497720807;T:650150631;N:222335 | 76 | 730230137 | 445929142 | 497720807 | 650150631 | 222335 | SRX22541614 | SRS19551199 | SRA1751942 | Bazzini Lab, Stowers Institute for Medical Research | Bazzini Lab, Stowers Institute for Medical Research | 1 | 0.91664 | 0.09242 | 0.85141 | 0.83766 | 76 | B | usable mapping rate | illumina | nextseq | 3prime | small_rna | lexogen | bulk | unknown | unknown | United States | 2023-11-15 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures |