|
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) |
GPL13310 |
Illumina HiSeq 2000 (Drosophila pseudoobscura) |
GPL16479 |
Illumina MiSeq (Drosophila melanogaster) |
|
Samples (30)
|
|
Relations |
BioProject |
PRJNA267532 |
SRA |
SRP049939 |
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 |
SRA Run Selector |
Processed data are available on Series record |
Raw data are available in SRA |