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Series GSE72709 Query DataSets for GSE72709
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
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.
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.
Contributor(s) Holwerda SJ, Dessus-Babus S, Stadler MB, Rijli F
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Submission date Sep 03, 2015
Last update date May 15, 2019
Contact name Tim Roloff
Organization name FMI
Department Functional Genomics
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (12)
GSM1868825 Cortex_RA_Hoxb5_1
GSM1868826 r5-6_WT_Hoxb5_1
GSM1868827 r5-6_RA_Hoxb5_1
This SubSeries is part of SuperSeries:
GSE72711 Hoxa5 dependent transcriptional regulation and RA-mediated Hox PG5 chromatin organization
BioProject PRJNA294818
SRA SRP063373

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
GSE72709_RAW.tar 5.5 Mb (http)(custom) TAR (of BEDGRAPH)
GSE72709_primers.xlsx 15.5 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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