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| Status |
Public on Sep 02, 2017 |
| Title |
Three Dimensional (3D) conformational change of chromatin organization upon RA mediated Hox PG5 induction |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
Changes in the transcriptional status of developmentally regulated genes, including Hox genes, go along with changes in the chromatin organisation as shown in cultured cells as well as in the developing embryo. The signals that affect the 3D structure of the genome are less understood. The tight regulation of Hox PG5 genes by RA might be accompanied by the physical separation of active and inactive Hox genes in the r5-6 and r8 domains in the hindbrain. To examine the role of RA on higher order chromatin conformation, we employed high-resolution circular chromosome conformation capture followed by high throughput sequencing (4C-Seq). We performed 4C-seq at E14.5, using the Hoxa5 and b5 promoters as view-points on Hox PG5 negative (rhombomers 5-6) and positive domains (rhombomer 8). 4C-seq was also performed with cortex as an entirely Hox negative control tissue.
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| Overall design |
12 samples were analysed. Two replicates for each tissue and treatment. The raw data for all samples in this series are contained in three fastq files associated with sample GSM1868848.
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| Contributor(s) |
Holwerda SJ, Dessus-Babus S, Stadler MB, Rijli F |
| Citation missing |
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| |
| Submission date |
Sep 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Tim Roloff |
| E-mail(s) |
tim.roloff@fmi.ch
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| Organization name |
FMI
|
| Department |
Functional Genomics
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| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE72711 |
Hoxa5 dependent transcriptional regulation and RA-mediated Hox PG5 chromatin organization |
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| Relations |
| BioProject |
PRJNA294818 |
| SRA |
SRP063373 |
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