An evaluation of the effects of CRISPR/cas9-mediated editing of the Dxz4 locus on regulation of the mouse inactive X chromosome in Patski cells [RNA-seq]
The mammalian inactive X chromosome (Xi) condenses into a bipartite structure with two superdomains of frequent long-range contacts separated by a boundary or hinge region. Using in situ DNase Hi-C in mouse cells with deletions or inversions within the hinge, we show that the conserved repeat locus Dxz4 alone is sufficient to maintain the bipartite structure and that Dxz4 orientation controls the distribution of long-range contacts on the Xi. Frequent long-range contacts between Dxz4 and the tel...
Provenance — who produced it, who reused it
Linked to 1 papers in the literature. Roles are inferred factual signals (who deposited the data vs who reused it), with counts — never a judgement about any author.
Deep data QC
96/100 · AStandardized, field-standard QC computed by touching the data — every metric states how it was obtained · evidence: measured
Bulk RNA-seq (mouse × spretus hybrid). Grade A: very good quality across measured metrics (Q30=89.4%, mean Q=33.4, duplication=12.8%, adapter=1.89%) for a hybrid species cross. Slightly lower base quality is acceptable given sequencing complexity of distinguishing between closely related genomes. The 75 bp reads and low duplication make this suitable for parent-of-origin and interspecies expression studies.
The A grade is a transparent weighted average. Each metric below scored from 0–100% against the published bulk-RNA-seq thresholds, weighted by its importance; nothing is hidden or subjective.
measured = computed from the data · extrapolated/reported = derived or from the repository · dq-1.0