Project description:We report the application of Chromosome Conformation Capture Carbon-copy (5C) to a 4.5 Mb stretch of the mouse X chromosome encompassing the X inactivation center locus. We uncover a series of discrete 200kb-1Mb topologically associating domains (TADs). These align with several domain-wide epigenomic features as well as co-regulated gene clusters. 5C analysis in EED and G9A mutants reveal that this segmental organisation in TADs does not relie on the underlying H3K27me3 or H3K9me2 blocks. Deletion of a boundary between two TADs leads to ectopic chromosomal contacts between them. Analysis of mESCs, mNPCs and MEFs suggest that the positioning of TADs on the chromosome is stable during cell differentiation though their internal organisation changes. Comparison of male (XY) and female (XX) differentiated cells highlights that the long-range chromosomal contacts within TADs are dampened on the inactive X compared to the active X. 5C oligonucleotides were designed around HindIII restriction site following an alternative scheme

2012-04-11 | E-GEOD-35721 | biostudies-arrayexpress

The German Cancer Research Center (DKFZ) Integrative Bioinformatics and Systems Biology (iBioS)

Project description:Organisation EGAO00000000029

| EGAO00000000029 | EGA

Spatial organisation of the X inactivation center

2012-04-11 | GSE35721 | GEO

Human ependymoma samples, Subgrouping [aCGH - German Cancer Research Center human 33K BAC array]

Project description:Whole-genome array comparative genomic hybridization (aCGH) of human ependymoma tumors. DOP-PCR products were spotted in triplicate onto NexterionTM Slide E epoxysilane-coated slides (PEQLAB, Erlangen, Germany) using a spotting robot (VersArray ChipWriterTM Pro system,BioRad, Munich, Germany) at 20C and 40% humidity. After spotting, slides were cross-linked,baked for 1 hr at 80C, and cross-linked again. Fresh frozen tumor material was collected during tumor resection. Copy number aberrations represent the status at diagnosis.

2011-08-14 | E-GEOD-27286 | biostudies-arrayexpress

DKFZ - German Cancer Research Centre

Project description:Organisation EGAO00000001147

| EGAO00000001147 | EGA