title: GSM2053975: mTXY-deltaA-nodox; Mus musculus; OTHER
library_construction_protocol: Hi-C:  Hi-C was performed as previously described (Lieberman-Aiden, E. et al. Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 326, 289–293 (2009), Naumova, N. et al. Organization of the Mitotic Chromosome. Science 342, 948–953 (2013), Belton JM et al., 2012 Methods). Briefly, Cells were lysed and chromatin was digested with HindIII, then digested ends were filled in with biotinylated dCTP  and ligated.  After reversing the formaldehyde crosslinks by incubation at 65 C  with Proteinase K overnight, unligated biotinylated ends were removed by incubation with T4 DNA polymerase.  RNA-Seq:  RNA-Seq was peformed as previously described (Gendrel, A.-V. et al. Developmental Dynamics and Disease Potential of Random Monoallelic Gene Expression. Dev. Cell 28, 366–380 (2014).). Hi-C:  Hi-C was performed as previously described (Lieberman-Aiden, E. et al. Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 326, 289–293 (2009), Naumova, N. et al. Organization of the Mitotic Chromosome. Science 342, 948–953 (2013)).  The ligation products were fragmented by Covaris sonication and then size selected by Ampure fractionation.  The DNA ends were prepared for Illumina sequencing adapter ligation by repairing the DNA ends and adding an ‘A’  to each end.  The biotinylated junctions were then pulled down using MyOne streptavidin beads. Illumina paired end adapters were ligated onto the DNA ends and then the fragments were PCR amplified.   Samples were sequenced on an Illumina HiSeq 2000 using either a PE50 or PE100 bp read (reads were truncated to 50bp during mapping).  RNA-Seq:  RNA-Seq was peformed as previously described (Gendrel, A.-V. et al. Developmental Dynamics and Disease Potential of Random Monoallelic Gene Expression. Dev. Cell 28, 366–380 (2014).).
attributes.tag: GEO Accession
attributes.value: GSM2053975