GSM3244821: Firre3p_4C_c13; Mus musculus; OTHER
We previously developed a modified 4C protocol (Chu et al., NSMB 2017)  to examine chromatin conformation from repetitive viewpoints. Our protocol has several advantages over existing 4C profiles: 1.) It sequences the genomic region amplified by the 4C primers, ensuring that on-target priming events can be identified and filtered from numerous off-target priming events 2.) Sequencing the viewpoint allows every read to be assigned to a particular allele if the viewpoint is near a variant, 3.) We use a random barcode to identify PCR duplicates, which previously has not been possible in 4C experiments. We performed our modified 4C using the protocol and analysis pipeline previously described for viewpoints within PAR-TERRA repeats (Chu et al., 2017). We used it for several viewpoints within Firre and Dxz4. Some viewpoints were in the core tandem repeats. For these viewpoints, we use the read outside the viewpoint for allelic determination. Others were in unique regions near the tandem repeats; for these we could use known variants to assign every read to the Xa or the Xi. We performed our analysis in two fibroblast lines, one where the mus X is inactive (mus Xi cas Xa), the other where the cas X is inactive (mus Xa cas Xi).
GEO Accession
GSM3244821