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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
63503 SRR17349051 SRX13523388 SRS11417518 SRP309488 PRJNA707026 Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos [RNA seq] GSE168359 Transcriptome Analysis Vertebrate embryos achieve developmental competency during zygotic genome activation ZGA by establishing chromatin states that silence yet poise developmental genes for subsequent lineage specific activation. Here we reveal how developmental gene poising is established de novo in preZGA zebrafish embryos. Poising is established at promoters and enhancers that initially contain open/permissive chromatin with 'Placeholder' nucleosomes bearing H2A.Z H3K4me1 and H3K27ac and DNA hypomethylation. Silencing is initiated by the recruitment of Polycomb Repressive Complex 1 PRC1 and H2Aub1 deposition by catalytic Rnf2 during preZGA and ZGA stages. During postZGA H2Aub1 enables Aebp2 containing PRC2 recruitment and H3K27me3 deposition. Notably preventing H2Aub1 via Rnf2 inhibition eliminates recruitment of Aebp2 PRC2 and H3K27me3 and elicits transcriptional upregulation of certain developmental genes during ZGA. However upregulation is independent of H3K27me3 – establishing H2Aub1 as the critical silencing modification at ZGA. Taken together we reveal the logic and mechanism for establishing poised/silent developmental genes in early vertebrate embryos. Overall design: RNA seq in early Zebrafish embryos. parent bioproject:PRJNA707023 pubmed:34982026   3.5hpf PRT4165 RNAseq rep3 GSM5761453   source name:WT Tubingen|strain:Tubingen|genotype:WT|developmental stage:3.5hpf|tissue:Whole body embryo|treatment:150uM PRT4165 3.5hpf PRT4165 RNAseq rep3 RNA seq fastq files were aligned to Zv10 using STAR v2.5.4a with the following settings: runMode alignReads twopassMode Basic alignIntronMax 50000 outSAMtype BAM SortedByCoordinate outWigType bedGraph outWigStrand Unstranded. BAM files were subsequently indexed using Samtools v1.8. FeatureCounts v1.5.1 was utilized to collect count data for zv10 Ensemble v90 genes via the following command: T 16 s 2 –largestOverlap. Count data for all replicates across experimental conditions were combined into a single count matrix in R. The count matrix was subsequently used to identify differentially expressed genes with the R package DESeq2 v1.18. For generation of bigwig files Bam files for a given condition were merged sorted and indexed with samtools. Subsequently deepTools bamCoverage v2.5.4 was used with the normlizeUsingRPKM option to produce bigwig files. Genome build: zv10 Supplementary files format and content: Text file and bigwig files. The count matrix contains data regarding the number of counts each experimental replicate has across zv10 Ensembl v90 transcripts. The bigwig files contain RNA seq signal normalized by RPKM. WT Tubingen Embryo media was supplemented with 150 μM PRT4165 or DMSO from when the embryos were at the 1 cell stage until the embryos were harvested. Total RNA was harvested from zebrafish embryos with a Qiagen Allprep kit Cat #80204. The Invitrogen DNA free DNA removal kit Cat # AM1906 was subsequently used to remove contaminating DNA from RNA samples. Intact polyA RNA was purified from total RNA samples 100 500 ng with oligodT magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit RS 122 2101 RS 122 2102. Standard zebrafish growth conditions. strain:Tubingen|genotype:WT|developmental stage:3.5hpf|tissue:Whole body embryo|treatment:150uM PRT4165 GSM5761453 GSM5761453: 3.5hpf PRT4165 RNAseq rep3; Danio rerio; RNA Seq GSM5761453   1 Total RNA was harvested from zebrafish embryos with a Qiagen Allprep kit Cat #80204. The Invitrogen DNA free DNA removal kit Cat # AM1906 was subsequently used to remove contaminating DNA from RNA samples. Intact polyA RNA was purified from total RNA samples 100 500 ng with oligodT magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit RS 122 2101 RS 122 2102. GEO Accession:GSM5761453 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP309488   loader:fastq load.py 19057X12_210803_A00421_0351_BHHFGTDSX2_S20_L001_R1_001.fastq.gz 19057X12_210803_A00421_0351_BHHFGTDSX2_S20_L001_R2_001.fastq.gz fastq fastq 11277505970.0 37342735.0 GSM5761453 r1 0:151 1:151 A:2802530584;C:2842552818;G:2728850469;T:2903416930;N:155169 151 151     2802530584 2842552818 2728850469 2903416930 155169 SRX13523388 SRS11417518 SRA1203419 GEO Cairns Lab, Oncological Sciences, University of Utah 2 0.80513 0.80511 0.01534 0.01516 0.80635 0.80541 0.48128 0.48761 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2021-12-28 Blastula Embryo Trunk Surface Structure