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11.4 years ago
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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):
- RNA sequencing of cancer reveals novel splicing alterations. Scientific Reports (http://www.nature.com/srep/2013/130422/srep01689/full/srep01689.html)
- 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
- Genome and Transcriptome Sequencing in Prospective Metastatic Triple-Negative Breast Cancer Uncovers Therapeutic Vulnerabilities. MCT (http://mct.aacrjournals.org/content/12/1/104.long)
- 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?
Welcome to scientific publishing as practised by most people :)
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.
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.
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