I’m going to quote in full the ”methods summary” from the latest FTO/IRX3 Nature paper (Smemo & al 2014); I think the paper is great and I’m only using it as an example of the format of Nature letters:

For 4C-seq, chromatin was digested with DpnII and Csp6I. Captured DNA was amplified using promoter-specific primers and deep sequenced.
For 3C, nuclei were digested with HindIII. Primer quality was assessed using serial dilutions of BACs encompassing the regions of interest (RP23-268O10, RP23-96F3). The average of four independent experiments is represented graphically (Extended data Fig 2c).

For anyone who hasn’t read the paper: it is not only about chromatin capture. The results rely on gene expression, reporter experiments in mice, phenotyping of knockout mice etc etc etc.

I read quite a lot of Nature and Science papers. Yes, one should be critical of the role of glamorous journals, but they publish a lot of things that either is interesting to me or get a lot of media attention. But the papers are not really papers, are they? They are too short to fit all the details, even with the additional online methods part. What does it say about a journal that it forces authors to cut out the methods, the most important section for judging reliability of the results? What does it say about me as a reader that I often don’t bother going to the supplementary material to read them? It’s not very flattering for any of us, I’m sure. If you suffer from such a shortage of paper that you have to remove a section of each article and hide it online it should be the discussion, not the methods.

Literature

Smemo & al (2014) Obesity-associated variants within FTO form long-range functional connections with IRX3.
Nature