User:Cornonthekaba/ATAC-seq/Bibliography

Buenrostro, Jason. ‘ATAC 􏰀seq: A Method for Assaying Chromatin Accessibility Genome􏰀 Wide’. Current Protocols in Molecular Biology 2015, no. 1 (2015): 21.29.1-21.29.9.


 * This is an in depth article with a lab procedure laid out. There is a mention of ATAC-seq and the requirement of Tn5 for the sequencing. There is a brief mention of compatibility for ATAC-seq which can also be useful.

Ma, S., Zhang, Y. Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq. Mol Biomed 1, 9 (2020).


 * This article provides information on technologies derived from the basic ATAC-sequencing techniques. Some of the technologies mentioned include fast-ATAC, omni-ATAC, and mini-ATAC. These new derivatives have created more specialized biological sequencing such as with blood work, frozen samples, and DNA purification, respectively. This article has a lot of information about the use of ATAC-seq and comes from a reliable journal.

Ou, J., Liu, H., Yu, J. et al. ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data. BMC Genomics 19, 169 (2018).


 * This article mentions the use of ATAC-seq on frozen samples and is an example of an experiment using ATAC-seq for analysis.

Yan, F., Powell, D.R., Curtis, D.J. et al. From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis. Genome Biol 21, 22 (2020).


 * This article mentions pros ad cons of using ATAC-seq and dives into the process of analyzing data successfully using ATAC-seq. The article could be helpful for a more general definition of ATAC-seq and what for what it actually serves a purpose.