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Series GSE38727 Query DataSets for GSE38727
Status Public on Nov 07, 2013
Title A common set of DNA regulatory elements shapes Drosophila appendages
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary We mapped open chromatin by FAIRE-seq and measured gene expression by RNA-seq in 3 types of Drosophila samples: staged whole embryos, imaginal discs, pharate appendages. We first demonstrate that regions of open chromatin precisely define regions of enhancer activity in developing embryos. In contrast to the dynamic changes in open chromatin observed between different stages of embryogenesis, we found that the open chromatin profiles in wing, leg, and haltere imaginal discs are nearly identical. This was also true again later in development, where the adult appendages also share nearly identical open chromatin profiles. Therefore, at a given developmental time point, different appendages are specified using a shared set of DNA regulatory elements. However, from one time point to the next, the set of accessible regulatory elements changes. Open chromatin profiles in appendage imaginal discs are almost entirely different than those of the adult appendages. We propose that master regulator transcription factors create morphologically distinct structures by differentially influencing the function of the same set of DNA regulatory modules.
 
Overall design Open chromatin profiling during Drosophila development: 3 stages of embryogenesis (2-replicates each); wing, leg, and haltere 3rd instar imaginal discs (3-replicates each); 3rd larval central nervous system (2-replicates); eye-antennal imaginal discs (2-replicates); wing, leg, and haltere pharate appendages (2-replicates each); Genomic DNA Inputs. Sequencing performed on Illumina GAII and HiSeq.
 
Contributor(s) McKay DJ, Lieb JD
Citation(s) 24229644, 29641560
Submission date Jun 14, 2012
Last update date Dec 10, 2019
Contact name Daniel J McKay
E-mail(s) dmckay1@email.unc.edu
Organization name The University of North Carolina at Chapel Hill
Department Biology, Genetics
Lab McKay Lab
Street address 3344 Genome Sciences Building
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7100
Country USA
 
Platforms (2)
GPL9061 Illumina Genome Analyzer II (Drosophila melanogaster)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (22)
GSM948712 e2-4hr_faire
GSM948713 e6-8hr_faire
GSM948714 e16-18hr_faire
Relations
BioProject PRJNA168643
SRA SRP013817

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
GSE38727_GEO_sumbission_mckay_12-17-13.xls.gz 40.5 Kb (ftp)(http) XLS
GSE38727_RAW.tar 245.8 Mb (http)(custom) TAR (of BED, WIG)
GSE38727_disc_geneName_cuffdiff_FPKMs.txt.gz 162.2 Kb (ftp)(http) TXT
GSE38727_embryo_geneName_cuffdiff_FPKMs.txt.gz 165.3 Kb (ftp)(http) TXT
GSE38727_pharate_geneNames_cuffdiff_FPKMs.txt.gz 163.8 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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