run_metadata: 51174
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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| 51174 | SRR8552566 | SRX5354324 | SRS4345542 | SRP184786 | PRJNA521558 | Brd4 and p300 confer transcriptional competency during zygotic genome activation | PRJNA521558 | Other | The awakening of the genome post fertilization is a cornerstone of animal development. However the mechanisms that activate the silent genome post fertilization are poorly understood. Here we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming. | ClickIT pulldown RNA seq ClickIT pulldown WT with chk1 treatment at 4h | ClickIT pulldown RNA seq 4h chk1 CiT AGN001959 | strain:TU/AB|age:4.0|dev stage:16 cell|sex:pooled male and female|tissue:embryo|treatment:chk1|molecule:RNA|selection:click it|sample ref:AGS001555|replicate ref:AGN001959|replicate order:1|BioSampleModel:Model organism or animal | ClickIT pulldown RNA seq ClickIT pulldown WT with chk1 treatment at 4h | AGR002643 | AGR002643 | RNA | OTHER | TRANSCRIPTOMIC | unspecified | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP184786 | AGR002643_R1.fastq.gz | fastq | 687656208.0 | 9048108.0 | AGR002643 R1.fastq.gz | 0:76 | A:169295405;C:170652179;G:163608326;T:184081751;N:18547 | 76 | 169295405 | 170652179 | 163608326 | 184081751 | 18547 | SRX5354324 | SRS4345542 | SRA847217 | Yale_Giraldez|Genetics | Yale_Giraldez_Group | 1 | 0.79745 | 0.19948 | 0.89514 | 0.85947 | 76 | B | usable mapping rate | illumina | hiseq_era | unknown | unknown | unknown | bulk | unknown | unknown | United States | 2019-06-12 | Cleavage | Embryo | Embryo Imprecise | All anatomical structures |