Training data for 'From peaks to gene' tutorial (Galaxy Training Material)

<p>The data provided here are part of a Galaxy Training Network tutorial that analyzes peaks from a study published by Li et al., 2012 (DOI:10.1016/j.stem.2012.04.023) to identify target genes</p

Additional file1: of Small RNA profiling of low biomass samples: identification and removal of contaminants

Figure S1. Scheme summarising the different control experiments, the titration experiments and their outcomes. a) Tracing non-human sRNA sequences to contaminants on spin columns by variation of different steps in the isolation protocol and analysis by qPCR assays. Modifications to the steps named at the top are listed below the workflow and the outcomes are summarised at the right hand side. b) Workflow of the titration experiment to determine a minimal safe input volume for all contaminant sequences. UCP column ultra-clean column. (PDF 86 kb

Additional file 5: of Small RNA profiling of low biomass samples: identification and removal of contaminants

Figure S4. Relative abundance of potential exogenous sRNAs in datasets derived from a plasma sample of one healthy individual. Detected levels of the 21 potential exogenous sRNA sequences in preparations using 45 to 1115 μL human plasma and regular or ultra-clean RNeasy spin columns and in controls without plasma, including no library, mock extractions and water controls (n = 33). cpm counts per million. Error bars indicate one standard deviation; data points are available in Additional file 2: Table S11. (PDF 11 kb

Additional file 3: of Small RNA profiling of low biomass samples: identification and removal of contaminants

Figure S2. Detection of contaminants in published datasets. Heatmap showing the relative abundances of the confirmed contaminant sequences in published sRNA sequencing data of low-biomass samples. Only samples for which any of the confirmed contaminants were detected are shown. Extraction methods: Q regular QIAGEN miRNeasy; T TRIZOL. rpm reads per million. (PDF 106 kb

Additional file 2: of Small RNA profiling of low biomass samples: identification and removal of contaminants

Table S1. List of the generated datasets with public accession numbers. Table S2. Analysed published datasets with references and public accession numbers. Table S3. Potential exogenous sRNA sequences detected in human plasma after removal of contaminants. Table S4. List of the prokaryotic species whose reference genomes were used in the initial analysis. Table S5. List of the eukaryotic species whose reference genomes and/or cDNA collections were used in the initial analysis. Table S6. List of the viruses whose reference genomes were used in the initial analysis. Table S7. Data points for Fig. 2a. Table S8. Data points for Fig. 2b. Table S9. Data points for Fig. 2c. Table S10. Data points for Fig. 2d. Table S11. Data points for Fig. 4a. Table S12. Data points for Fig. 5b. (XLSX 228 kb

Additional file 4: of Small RNA profiling of low biomass samples: identification and removal of contaminants

Figure S3. Detection of contaminants in eluates of regular and ultra-clean RNeasy columns. Two batches of regular miRNeasy columns and four batches of ultra-clean RNeasy columns were compared. Results are based on sRNA sequencing data of mock extracts, normalised to the detected levels of spike-in synthetic RNAs. The different shadings represent reads mapping to the human genome with 2, 1, or 0 mismatches and the different column batches are coloured in the same colours as in main Fig. 3, as indicated in the legends. (PDF 16 kb