If you are using Custom CDF probe mapping files, please, cite:

  Manhong Dai and Pinglang Wang and Andrew D Boyd and Georgi Kostov and
  Brian Athey and Edward G Jones and William E Bunney and Richard M
  Myers and Terry P Speed and Huda Akil and Stanley J Watson and Fan
  Meng Evolving gene/transcript definitions significantly alter the
  interpretation of GeneChip data. Nucleic Acids Research 33(20):e175,
  2005. DOI: 10.1093/nar/gni179.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Manhong Dai and Pinglang Wang and Andrew D Boyd and Georgi Kostov and Brian Athey and Edward G Jones and William E Bunney and Richard M Myers and Terry P Speed and Huda Akil and Stanley J Watson and Fan Meng},
    title = {{E}volving gene/transcript definitions significantly alter the interpretation
	of {G}ene{C}hip data.},
    journal = {Nucleic Acids Research},
    year = {2005},
    volume = {33},
    pages = {e175},
    number = {20},
    url = {http://dx.doi.org/10.1093/nar/gni179},
  }

The sample BAM files contain a subset of reads from this publication:

  John C Marioni and Christopher E Mason and Shrikant M Mane and
  Matthew Stephens and Yoav Gilad {RNA}-seq: an assessment of technical
  reproducibility and comparison with gene expression arrays. Genome
  Research 18(9):1509-1517, 2008. DOI: 10.1101/gr.079558.108.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {John C Marioni and Christopher E Mason and Shrikant M Mane and Matthew Stephens and Yoav Gilad},
    title = {{RNA}-seq: an assessment of technical reproducibility and comparison
	with gene expression arrays.},
    journal = {Genome Research},
    year = {2008},
    volume = {18},
    pages = {1509-1517},
    number = {9},
    url = {http://dx.doi.org/10.1101/gr.079558.108},
  }