Quantitation of human sperm DNA accessibility and DNA nicking by NicE-view and Nick translation imaging

Accessible or nicked DNA from human sperm was labelled using NicE-view, ATAC-See or nick translation.

For nick translation and NicE-view 60 individuals were profiled, for 57 of these individuals two samples were available (1 for total sperm and 1 for sperm selected for motility via the swim-up method), while for the final 3 only total sperm was available (filename: Gill_NicE_view_CellProfiler.csv).

For ATAC-See data from 5 individuals were generated (Gill_ATAC_See_CellProfiler.csv).

For a further 6 individuals sperm were isolated by FACS following labelling with the DNA dye CMA3 and subjected to T4 NicE-view (Gill_NicE_view_CMA3_Cell_Profiler.csv).

Finally a data set containing double labelling of DNA nicks and DNA accessibility was generated for 6 individuals (Gill NicE_view_Double_Labelling_CellProfiler.csv).

For each sample 400 Z-projections were generated and quantified using CellProfiler. Data are saved in .csv files.

A further .csv file contains metadata relating to demographic, hormonal and reproductive parameters of the study participants (Gill_NicE_view_participant.csv).

A series of 13 R scripts (number 01-12, and a general script containing helper functions) are included to analyze the data and generate the figures found in Gill et al. (A text file containing instructions regarding directory structures is also included) as a .zip archive