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Series GSE83851 Query DataSets for GSE83851
Status Public on Nov 22, 2016
Title ATAC-seq analysis of chromatin accessibility and nucleosome positioning in Drosophila melanogaster precellular blastoderm embryos
Organism Drosophila melanogaster
Experiment type Other
Summary Purpose: The goal of this study was to measure how chromatin accessibility and nucleosome positioning changes as embryos undergo the midblastula transition (MBT).

Methods: Single or paired embryos were collected at three minute intervals over the three cell cycles leading up to the MBT (nuclear cycles 11, 12, and 13). Embryos were subjected to ATAC-seq library preparation following established protocols. Thirteen total timepoints were collected. At least three biological replicates were collected per timepoint. Samples were subjected to paired end sequencing on an Illumina HiSeq 2500. Wild type (diploid) embryos were compared with haploid (sesame) embryos to determine whether changes in chromatin accessibility are governed by measurement of the nucleo-cytoplasmic ratio, a well known biological timer that controls the onset of the MBT.

Results: Chromatin accessibility changes dynamically during the period leading up to the MBT. Initially, genomic enhancer elements are accessible, but during NC12 and NC13, large scale chromatin remodeling results in a gain of accessibility for promoter elements and insulators. A substantial fraction of the dynamic chromatin accessibility is temporally regulated by the mechanism that measures the embryonic nuclear-cytoplasmic ratio, as determined by comparison between haploid and diploid embryos. A substantial fraction of open chromatin regions remain 'accessible' during mitotic metaphase.
Overall design Embryos were collected in a three minute time course spanning three cell cycles and prepared for ATAC seq analysis. Triplicate biological replicates were collected per timepoint. Samples were subjected to paired end sequencing (2x 67bp) on an Illumina HiSeq 2500.

Please note that replicates were pooled for generating processed files, and each processed data file is linked to the first replicate sample (of the corresponding samples) (*_rep1).
Contributor(s) Blythe SA, Wieschaus EF
Citation(s) 27879204
NIH grant(s)
Grant ID Grant title Affiliation Name
F32 HD072653 Mechanisms for Measuring the Nucleocytoplasmic Ratio in Early Embryogenesis PRINCETON UNIVERSITY BLYTHE
R37 HD015587 Oogenesis and Early Embryogenesis in Drosophila PRINCETON UNIVERSITY WIESCHAUS
Submission date Jun 29, 2016
Last update date May 15, 2019
Contact name Shelby A Blythe
Organization name Northwestern University
Department Molecular Biosciences
Lab Blythe
Street address Northwestern University, Hogan Hall, 2205 Tech Drive
City Evanston
State/province IL
ZIP/Postal code 60208
Country USA
Platforms (1)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
Samples (81)
GSM2219678 WT_15121502_NC11_03_rep1
GSM2219679 WT_15121602_NC11_03_rep2
GSM2219680 WT_15121802_NC11_03_rep3
BioProject PRJNA327205
SRA SRP077569

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 280.0 Kb (ftp)(http) TXT
GSE83851_RAW.tar 6.1 Gb (http)(custom) TAR (of BED, BEDGRAPH, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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