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Series GSE50771 Query DataSets for GSE50771
Status Public on Sep 12, 2013
Title Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 2)
Organisms Drosophila melanogaster; Drosophila pseudoobscura; Drosophila virilis
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary To better characterize how variation in regulatory sequences drives divergence in gene expression, we undertook a systematic study of transcription factor binding and gene expression in blastoderm embryos of four species, which sample much of the diversity in the 40 million-year old genus Drosophila: D. melanogaster, D. yakuba, D. pseudoobscura and D. virilis. We compared gene expression, measured by mRNA-seq, to the genome-wide binding, measured by ChIP-seq, of four transcription factors involved in early anterior-posterior patterning. We found that mRNA levels are much better conserved than individual transcription factor binding events, and that changes in a gene’s expression were poorly explained by changes in adjacent transcription factor binding. However highly bound sites, sites in regions bound by multiple factors and sites near genes are conserved more frequently than other binding, suggesting that a considerable amount of transcription factor binding is weakly or non-functional and not subject to purifying selection
 
Overall design Comparison of the evolution of gene expression and regulatory TF binding in early Drosophila embryos.
 
Contributor(s) Paris M, Kaplan T, Li X, Villalta JE, Lott SE, Eisen MB
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Submission date Sep 11, 2013
Last update date May 15, 2019
Contact name Mathilde PARIS
E-mail(s) thildeparis@gmail.com
Organization name CNRS
Department Institut de Genomique Fonctionnelle de Lyon
Street address 32-34 avenue Tony Garnier
City Lyon
ZIP/Postal code 69006
Country France
 
Platforms (3)
GPL9061 Illumina Genome Analyzer II (Drosophila melanogaster)
GPL17715 Illumina Genome Analyzer II (Drosophila melanogaster; Drosophila pseudoobscura; Drosophila virilis)
GPL17717 Illumina HiSeq 2000 (Drosophila melanogaster; Drosophila pseudoobscura; Drosophila virilis)
Samples (16)
GSM1228844 Dmel_Input_2
GSM1228845 Dmel_Input_3
GSM1228846 Dmel_Input_4
This SubSeries is part of SuperSeries:
GSE50773 Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression
Relations
BioProject PRJNA218869
SRA SRP029885

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
GSE50771_ChIP_metatable_BCD.txt.gz 173.3 Kb (ftp)(http) TXT
GSE50771_ChIP_metatable_GT.txt.gz 361.5 Kb (ftp)(http) TXT
GSE50771_ChIP_metatable_HB.txt.gz 431.5 Kb (ftp)(http) TXT
GSE50771_ChIP_metatable_KR.txt.gz 450.0 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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