The first published paper on RNA-seq: Setting the record straight

What is the first published paper that used RNA-Seq to study transcriptome? Take any recent (almost?) RNA-Seq paper, the two papers that get cited for RNA-Seq technology are

No doubt, they are great papers, but just found from a comment by Joe Ecker from Salk Institute at Lior Pachter’s blog that Joe Ecker’s group was the first to publish a paper using RNA-Seq technology. The paper was published in Cell and beats the above mentioned publications by a month.

The paper by Lister et. al. not just did RNA-Seq, but also small RNA-seq and methylC-seq in Arabidopsis.

It is bit embarrassing to miss like this on a new technology at this age of internet. Here is the list of dates for the three publications. Also check the comments for an earlier paper that used “EST related terminology” instead of RNA-seq.

Lister et. al. Cell

  • Received: 19 February 2008,
  • Revised: 20 March 2008,
  • Accepted 27 March 2008,
  • Available online: 17 April 2008
  • Published online: 17 April 2008
  • Published in Print: 2 May 2008

Nagalakshmi et. al. Science

  • Received: 31 March 2008;
  • Accepted: 22 April 2008
  • Published online: 1 May 2008;
  • Published in Print: 6 June 2008

Mortazavi et. al. Nature Methods:

  • Received: 2 May 2008
  • Accepted: 27 May
  • Published Online: 30 May 2008
  • Published in Print: July 2008




  1. John Thompson says:

    In fact, there are 2 other papers submitted prior to Nagalakshmi et al and Mortazavi et al though both were submitted after the Lister paper. See Wilhem et al (2008) Nature doi:10.1038/nature07002 and Cloonan et al (2008) Nature Methods DOI:10.1038/NMETH.1223. All discussed in News and Views by Jay Shendure in same issue of Nature Methods.

  2. Paul McGettigan says:

    The Bainbridge et al BMC Genomics 2006 paper beats the above – they used 454 and used a lot of EST related terminology in their paper but it is RNA-seq.


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