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GEO help: Mouse over screen elements for information. |
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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
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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.
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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.
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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
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Organization name |
The University of North Carolina at Chapel Hill
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Department |
Biology, Genetics
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Lab |
McKay Lab
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Street address |
3344 Genome Sciences Building
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City |
Chapel Hill |
State/province |
NC |
ZIP/Postal code |
27599-7100 |
Country |
USA |
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Platforms (2) |
GPL9061 |
Illumina Genome Analyzer II (Drosophila melanogaster) |
GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
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Samples (22)
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Relations |
BioProject |
PRJNA168643 |
SRA |
SRP013817 |
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 |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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