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Series GSE63333 Query DataSets for GSE63333
Status Public on Nov 18, 2014
Title Genome-wide binding patterns of group B Sox proteins in four Drosophila species
Organisms Drosophila melanogaster; Drosophila pseudoobscura; Drosophila simulans; Drosophila yakuba
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We used DamID-seq to analyze the genome-wide binding patterns of the group B Sox proteins Dichaete and SoxNeuro in four species of Drosophila: D. melanogaster, D. simulans, D. yakuba and D. pseudoobscura. Both binding site turnover between species and a comparison of the binding properties of the two partially-redundant transcription factors were analyzed. We found that, despite widespread turnover, genomic intervals that are commonly bound by both Dichaete and SoxNeuro are highly conserved in Drosophila.
 
Overall design DamID for Dichaete (Dichaete-Dam) was performed in D. melanogaster, D. simulans, D. yakuba and D. pseudoobscura, while DamID for SoxNeuro (SoxN-Dam) was performed in D. melanogaster and D. simulans. The control experiment, Dam-only, was performed in all species. Three biological replicates were sequenced for each condition in each species.
 
Contributor(s) Carl SH, Russell S
Citation(s) 25887553
Submission date Nov 17, 2014
Last update date May 15, 2019
Contact name Sarah Carl
E-mail(s) sarah.carl@fmi.ch
Organization name Friedrich Miescher Institute
Department Epigenetics
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platforms (5)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
GPL13306 Illumina HiSeq 2000 (Drosophila simulans)
GPL13307 Illumina HiSeq 2000 (Drosophila yakuba)
Samples (30)
GSM1545885 Dmel_DichaeteDam_rep1
GSM1545886 Dmel_DichaeteDam_rep2
GSM1545887 Dmel_DichaeteDam_rep3
Relations
BioProject PRJNA267532
SRA SRP049939

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
GSE63333_Dmel_DDam_DESeq2_allGATC.bedgraph.gz 4.6 Mb (ftp)(http) BEDGRAPH
GSE63333_Dmel_DDam_DESeq2_p01_merged.bed.gz 150.8 Kb (ftp)(http) BED
GSE63333_Dmel_DDam_DESeq2_p05_merged.bed.gz 179.0 Kb (ftp)(http) BED
GSE63333_Dmel_SoxNDam_DESeq2_allGATC.bedgraph.gz 4.6 Mb (ftp)(http) BEDGRAPH
GSE63333_Dmel_SoxNDam_DESeq2_p01_merged.bed.gz 152.1 Kb (ftp)(http) BED
GSE63333_Dmel_SoxNDam_DESeq2_p05_merged.bed.gz 195.6 Kb (ftp)(http) BED
GSE63333_Dpse_DDam_DESeq2_allGATC.bedgraph.gz 4.8 Mb (ftp)(http) BEDGRAPH
GSE63333_Dpse_DDam_DESeq2_p05_merged.bed.gz 26.2 Kb (ftp)(http) BED
GSE63333_Dpse_DDam_dm3_DESeq2_allGATC.bedgraph.gz 4.0 Mb (ftp)(http) BEDGRAPH
GSE63333_Dpse_DDam_dm3_DESeq2_p05_merged.bed.gz 17.9 Kb (ftp)(http) BED
GSE63333_Dsim_DDam_DESeq2_allGATC.bedgraph.gz 4.7 Mb (ftp)(http) BEDGRAPH
GSE63333_Dsim_DDam_DESeq2_p05_merged.bed.gz 153.0 Kb (ftp)(http) BED
GSE63333_Dsim_DDam_dm3_DESeq2_allGATC.bedgraph.gz 4.1 Mb (ftp)(http) BEDGRAPH
GSE63333_Dsim_DDam_dm3_DESeq2_p05_merged.bed.gz 137.4 Kb (ftp)(http) BED
GSE63333_Dsim_SoxNDam_DESeq2_allGATC.bedgraph.gz 4.6 Mb (ftp)(http) BEDGRAPH
GSE63333_Dsim_SoxNDam_DESeq2_p05_merged.bed.gz 149.3 Kb (ftp)(http) BED
GSE63333_Dsim_SoxNDam_dm3_DESeq2_allGATC.bedgraph.gz 4.0 Mb (ftp)(http) BEDGRAPH
GSE63333_Dsim_SoxNDam_dm3_DESeq2_p05_merged.bed.gz 130.4 Kb (ftp)(http) BED
GSE63333_Dyak_DDam_DESeq2_allGATC.bedgraph.gz 5.1 Mb (ftp)(http) BEDGRAPH
GSE63333_Dyak_DDam_DESeq2_p05_merged.bed.gz 229.2 Kb (ftp)(http) BED
GSE63333_Dyak_DDam_dm3_DESeq2_allGATC.bedgraph.gz 4.1 Mb (ftp)(http) BEDGRAPH
GSE63333_Dyak_DDam_dm3_DESeq2_p05_merged.bed.gz 182.4 Kb (ftp)(http) BED
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