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?