Series Summary for DCD000228SR

MNase-sequencing of 256-cell and dome embryos to reveal nucleosome organization at promoters during genome activation

Survey

10.1101/gr.157750.113

GSE44269

The organization of nucleosomes influences transcriptional activity by controlling accessibility of DNA binding proteins to the genome. Genome-wide nucleosome binding profiles have identified a canonical nucleosome organization at gene promoters, where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. The mechanisms of formation and the function of canonical promoter nucleosome organization remain unclear. Here we analyze the genome-wide location of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear on thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization is independent of DNA sequence preference, transcriptional elongation, and robust RNA polymerase II (Pol II) binding. Instead, canonical promoter nucleosome organization correlates with the presence of Histone H3 Lysine 4 trimethylation (H3K4me3) and affects future transcriptional activation. These findings reveal that genome activation is central to the organization of nucleosome arrays during early embryogenesis

True

palfy

June 13, 2016, 1:28 a.m.

Nov. 7, 2018, 5:18 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006633BS DCD000228SR whole organism Schier Lab, Harvard University AB/TL Dome 4.3
Applied Assay ID Biosample Replicate Assay
DCD001391AA DCD012885BR MNase-seq_Schier_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001184SQ DCD001402TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000834DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001389AA DCD012887BR MNase-seq_Schier_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001186SQ DCD001414TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000833DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001173SQ DCD001413TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000832DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001179SQ DCD001412TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000831DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001185SQ DCD001411TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000830DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001180SQ DCD001410TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000829DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001187SQ DCD001409TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000828DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001176SQ DCD001408TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000827DT: FASTQ
DCD009122DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002378AA DCD013889BR ChIP-seq_Schier_Lab_Pol_II_8WG16_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002751SQ DCD002783TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD010783DT: FASTQ
DCD016370DT: BAM GRCz11/danRer11
DCD016371DT: BED GRCz11/danRer11
DCD016372DT: BIGNARROWPEAK GRCz11/danRer11
DCD016373DT: BIGNARROWPEAK GRCz11/danRer11
DCD016375DT: BIGWIG GRCz11/danRer11
DCD016686DT: BED GRCz10/danRer10
DCD016687DT: BIGNARROWPEAK GRCz10/danRer10
DCD016688DT: BIGNARROWPEAK GRCz10/danRer10
DCD016692DT: BAM GRCz10/danRer10
DCD017086DT: BED GRCz10/danRer10
DCD017088DT: BAM GRCz10/danRer10
DCD017089DT: BIGNARROWPEAK GRCz10/danRer10
DCD017090DT: BIGNARROWPEAK GRCz10/danRer10
DCD017093DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002377AA DCD013890BR ChIP-seq_Schier_Lab_Pol_II_4H8_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002757SQ DCD002781TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD010784DT: FASTQ
DCD016315DT: BED GRCz11/danRer11
DCD016316DT: BAM GRCz11/danRer11
DCD016317DT: BIGNARROWPEAK GRCz11/danRer11
DCD016318DT: BIGNARROWPEAK GRCz11/danRer11
DCD016319DT: BIGWIG GRCz11/danRer11
DCD016662DT: BIGNARROWPEAK GRCz10/danRer10
DCD016663DT: BIGNARROWPEAK GRCz10/danRer10
DCD016664DT: BED GRCz10/danRer10
DCD016666DT: BAM GRCz10/danRer10
DCD017056DT: BIGNARROWPEAK GRCz10/danRer10
DCD017058DT: BED GRCz10/danRer10
DCD017059DT: BAM GRCz10/danRer10
DCD017060DT: BIGNARROWPEAK GRCz10/danRer10
DCD017064DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002381AA DCD013892BR ChIP-seq_Schier_Lab_H3K4me3_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002752SQ DCD002777TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD010787DT: FASTQ
DCD016489DT: BED GRCz11/danRer11
DCD016491DT: BIGNARROWPEAK GRCz11/danRer11
DCD016492DT: BIGNARROWPEAK GRCz11/danRer11
DCD016493DT: BAM GRCz11/danRer11
DCD016494DT: BIGWIG GRCz11/danRer11
DCD016682DT: BED GRCz10/danRer10
DCD016683DT: BAM GRCz10/danRer10
DCD016684DT: BIGNARROWPEAK GRCz10/danRer10
DCD016685DT: BIGNARROWPEAK GRCz10/danRer10
DCD017082DT: BAM GRCz10/danRer10
DCD017083DT: BIGNARROWPEAK GRCz10/danRer10
DCD017084DT: BIGNARROWPEAK GRCz10/danRer10
DCD017085DT: BED GRCz10/danRer10
DCD017087DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002380AA DCD013893BR ChIP-seq_Schier_Lab_H3K36me3_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002754SQ DCD002778TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD010785DT: FASTQ
DCD016320DT: BIGNARROWPEAK GRCz11/danRer11
DCD016321DT: BED GRCz11/danRer11
DCD016322DT: BAM GRCz11/danRer11
DCD016323DT: BIGNARROWPEAK GRCz11/danRer11
DCD016327DT: BIGWIG GRCz11/danRer11
DCD016654DT: BED GRCz10/danRer10
DCD016655DT: BAM GRCz10/danRer10
DCD016656DT: BIGNARROWPEAK GRCz10/danRer10
DCD016657DT: BIGNARROWPEAK GRCz10/danRer10
DCD017047DT: BAM GRCz10/danRer10
DCD017048DT: BIGNARROWPEAK GRCz10/danRer10
DCD017049DT: BIGNARROWPEAK GRCz10/danRer10
DCD017051DT: BED GRCz10/danRer10
DCD017053DT: BIGWIG GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD002379AA DCD013894BR ChIP-seq_Schier_Lab_H3K27me3_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002753SQ DCD002779TR Schier Lab, Harvard University Illumina HiSeq 1000 unstranded 10/18/2013
DCD010786DT: FASTQ
DCD016330DT: BIGNARROWPEAK GRCz11/danRer11
DCD016331DT: BIGNARROWPEAK GRCz11/danRer11
DCD016332DT: BED GRCz11/danRer11
DCD016333DT: BAM GRCz11/danRer11
DCD016334DT: BIGWIG GRCz11/danRer11
DCD016658DT: BED GRCz10/danRer10
DCD016659DT: BIGNARROWPEAK GRCz10/danRer10
DCD016660DT: BAM GRCz10/danRer10
DCD016661DT: BIGNARROWPEAK GRCz10/danRer10
DCD017050DT: BED GRCz10/danRer10
DCD017052DT: BAM GRCz10/danRer10
DCD017054DT: BIGNARROWPEAK GRCz10/danRer10
DCD017055DT: BIGNARROWPEAK GRCz10/danRer10
DCD017057DT: BIGWIG GRCz10/danRer10
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006634BS DCD000228SR whole organism Schier Lab, Harvard University AB/TL 256-cell 2.5
Applied Assay ID Biosample Replicate Assay
DCD001392AA DCD012886BR MNase-seq_Schier_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001177SQ DCD001404TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000842DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001390AA DCD012888BR MNase-seq_Schier_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD001174SQ DCD001407TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded — 10/18/2013
DCD000835DT: FASTQ
DCD009121DT: BIGWIG GRCz10/danRer10
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001183SQ DCD001406TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000839DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001188SQ DCD001405TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000838DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001175SQ DCD001403TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000836DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001178SQ DCD001401TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000837DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001181SQ DCD001400TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000841DT: FASTQ
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001182SQ DCD001399TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 10/18/2013
DCD000840DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD002374AA DCD013891BR RNA-seq_Schier_Lab_0011AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD002756SQ DCD002780TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 76 10/18/2013
DCD010780DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD002376AA DCD013895BR ChIP-seq_Schier_Lab_H3K4me3_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD002758SQ DCD002782TR Schier Lab, Harvard University Illumina HiSeq 2000 unstranded 147 10/18/2013
DCD010781DT: FASTQ
DCD016270DT: BAM GRCz11/danRer11
DCD016271DT: BED GRCz11/danRer11
DCD016272DT: BIGNARROWPEAK GRCz11/danRer11
DCD016275DT: BIGNARROWPEAK GRCz11/danRer11
DCD016276DT: BIGWIG GRCz11/danRer11
DCD016650DT: BIGNARROWPEAK GRCz10/danRer10
DCD016651DT: BIGNARROWPEAK GRCz10/danRer10
DCD016652DT: BED GRCz10/danRer10
DCD016653DT: BAM GRCz10/danRer10
DCD017042DT: BIGWIG GRCz10/danRer10
DCD017043DT: BIGNARROWPEAK GRCz10/danRer10
DCD017044DT: BIGNARROWPEAK GRCz10/danRer10
DCD017045DT: BED GRCz10/danRer10
DCD017046DT: BAM GRCz10/danRer10
Biosample ID Series biosample_type biosample_lab genetic_background stage Controlled By anatomical_term Treatment Hours Post Fertilization Mutation Description
DCD007150BS DCD000228SR whole organism Schier Lab, Harvard University AB/TL Oblong — — 3.6 —
Applied Assay ID Biosample Replicate Assay Controlled By
DCD002375AA DCD013888BR ChIP-seq_Schier_Lab_H3K4me3_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Chemistry Version Paired End Strand Maximum Read Length Sequencing Date
DCD002755SQ DCD002776TR Schier Lab, Harvard University Illumina HiSeq 2000 — ✘ unstranded 147 10/18/2013
DCD010782DT: FASTQ
DCD016305DT: BED GRCz11/danRer11
DCD016306DT: BAM GRCz11/danRer11
DCD016307DT: BIGNARROWPEAK GRCz11/danRer11
DCD016308DT: BIGNARROWPEAK GRCz11/danRer11
DCD016309DT: BIGWIG GRCz11/danRer11
DCD016676DT: BAM GRCz10/danRer10
DCD016678DT: BIGNARROWPEAK GRCz10/danRer10
DCD016679DT: BIGNARROWPEAK GRCz10/danRer10
DCD016680DT: BED GRCz10/danRer10
DCD017077DT: BIGNARROWPEAK GRCz10/danRer10
DCD017078DT: BIGNARROWPEAK GRCz10/danRer10
DCD017079DT: BED GRCz10/danRer10
DCD017080DT: BIGWIG GRCz10/danRer10
DCD017081DT: BAM GRCz10/danRer10