Question: How To Find Rna-Seq Data Of Published Papers?
6
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6.9 years ago by
user850
United States
user850 wrote:

where can one find RNA-seq data of published papers? The following three papers have large RNA-seq data sets in open-access journals but as far as I can tell there's no mention of actual RNA-seq data files availability (no link to GEO or SRA):

  1. RNA sequencing of cancer reveals novel splicing alterations. Scientific Reports (http://www.nature.com/srep/2013/130422/srep01689/full/srep01689.html)
  2. Whole transcriptome RNA-Seq analysis of breast cancer recurrence risk using formalin-fixed paraffin-embedded tumor tissue. PLoS One http://www.ncbi.nlm.nih.gov/pubmed/22808097
  3. Genome and Transcriptome Sequencing in Prospective Metastatic Triple-Negative Breast Cancer Uncovers Therapeutic Vulnerabilities. MCT (http://mct.aacrjournals.org/content/12/1/104.long)
  4. A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. NAR (http://nar.oxfordjournals.org/content/early/2011/05/27/nar.gkr362.full)

The 4th paper says that they sequenced 22 breast cancer cell lines and used an additional set of 9 rna-seq samples but where is the data? From abstract: "We applied SnowShoes-FTD to identify 50 fusion candidates in 22 breast cancer and 9 non-transformed cell lines".

I cannot find the sequence files for these anywhere but thought this is a basic prerequisite for publishing in an open access journal. Where is all the data?

ADD COMMENTlink modified 6.9 years ago • written 6.9 years ago by user850
6

Welcome to scientific publishing as practised by most people :)

ADD REPLYlink written 6.9 years ago by Neilfws48k
4

Sadly enough, sometimes authors and journals fail to comply to some basic prerequisite. I hope not to go OT if I add my experience with PNAS, where I am interested in the paper "Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood" (http://www.pnas.org/content/early/2008/10/03/0808319105.full.pdf+html) In that case authors (Fan, Blumenfeld, Chitkara, Hudgins and Quake) published an SRA accession, but the accession itself doesn't exist. I contacted the corresponding author and received no response. I then contacted PNAS and they told me (less than two weeks ago) that they would contact the authors and require them to make data available. I suggest that you write to the authors and the journals asking kindly but firmly that they share their data (especially if the journals have a prerequisite of making data public. I am pretty sure that PLoS one does...). In my case, I will allow some time to make data available and I will then insist. If the authors have some good reason not to share their data I will be happy to hear them.

ADD REPLYlink written 6.9 years ago by Fabio Marroni2.5k
2

To follow up on what Fabio Marroni writes here, I would at first contact the authors for their datasets. If they do not respond then I would contact the corresponding editor of the paper or the managing editor of the journal. After this you might be out of luck -- except to complain to the journal to insist they require authors to submit data for future paper submissions.

ADD REPLYlink written 6.9 years ago by Josh Herr5.7k

Are journals generally responsive to this though? Can't they say - it's up to the authors? I'd find that absurd but just wondering if it happens

ADD REPLYlink written 6.9 years ago by user850
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