Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues.

The use of Assay for Transposase-Accessible Chromatin (ATAC-seq) to profile chromatin accessibility has surged over the past years, but its applicability to tissues has been very limited. With the intent of preserving nuclear architecture during long-term storage, cryopreserved nuclei preparations from chicken lung were used to optimize ATAC-seq. Sequencing data were compared with existing DNase-seq, ChIP-seq, and RNA-seq data to evaluate library quality, ultimately resulting in a modified ATAC-seq method capable of generating high quality chromatin accessibility data from cryopreserved nuclei preparations. Using this method, nucleosome-free regions (NFR) identified in chicken lung overlapped half of DNase-I hypersensitive sites, coincided with active histone modifications, and specifically marked actively expressed genes. Notably, sequencing only the subnucleosomal fraction dramatically improved signal, while separation of subnucleosomal reads post-sequencing did not improve signal or peak calling. The broader applicability of this modified ATAC-seq technique was tested using cryopreserved nuclei preparations from pig tissues, resulting in NFR that were highly consistent among biological replicates. Furthermore, tissue-specific NFR were enriched for binding motifs of transcription factors related to tissue-specific functions, and marked genes functionally enriched for tissue-specific processes. Overall, these results provide insights into the optimization of ATAC-seq and a platform for profiling open chromatin in animal tissues

Temperature determination via STJ optical spectroscopy

ESA's Superconducting Tunnel Junction (STJ) optical photon-counting camera (S-Cam2) incorporates an array of pixels with intrinsic energy sensitivity. Using the spectral fitting technique common in X-ray astronomy, we fit black bodies to nine stellar spectra, ranging from cool flare stars to hot white dwarfs. The measured temperatures are consistent with literature values at the expected level of accuracy based on the predicted gain stability of the instrument. Having also demonstrated that systematic effects due to count rate are likely to be small, we then proceed to apply the temperature determination method to four cataclysmic variable (CV) binary systems. In three cases we measure the temperature of the accretion stream, while in the fourth we measure the temperature of the white dwarf. The results are discussed in the context of existing CV results. We conclude by outlining the prospects for future versions of S-Cam.Comment: 9 pages, 9 figures (11 files); uses aa.cls; accepted for publication in A&