Additional file 1 of Determining breast cancer histological grade from RNA-sequencing data

All additional figures and tables listed. (PDF 488 kb

Additional file 2 of Determining breast cancer histological grade from RNA-sequencing data

Includes lists of genes and coefficients of each model. (XLSX 1361 kb

Concordance of heterozygous SNPs (lines with dots) for 100 ng and 1 µg exome libraries of different multiplexity and a 500 ng 96-plex target capture library.

<p>The average concordance for exome libraries was 99.4% with no significant difference between libraries. For the 96-plex experiment, the average concordance was 99.8%. Solid lines indicate the average allelic balance. Even in the 96-plex experiment, no bias in allelic balance is observed.</p

Library Preparation and Multiplex Capture for Massive Parallel Sequencing Applications Made Efficient and Easy

<div><p>During the recent years, rapid development of sequencing technologies and a competitive market has enabled researchers to perform massive sequencing projects at a reasonable cost. As the price for the actual sequencing reactions drops, enabling more samples to be sequenced, the relative price for preparing libraries gets larger and the practical laboratory work becomes complex and tedious. We present a cost-effective strategy for simplified library preparation compatible with both whole genome- and targeted sequencing experiments. An optimized enzyme composition and reaction buffer reduces the number of required clean-up steps and allows for usage of bulk enzymes which makes the whole process cheap, efficient and simple. We also present a two-tagging strategy, which allows for multiplex sequencing of targeted regions. To prove our concept, we have prepared libraries for low-pass sequencing from 100 ng DNA, performed 2-, 4- and 8-plex exome capture and a 96-plex capture of a 500 kb region. In all samples we see a high concordance (>99.4%) of SNP calls when comparing to commercially available SNP-chip platforms.</p> </div

Additional file 6: of Expression levels of long non-coding RNAs are prognostic for AML outcome

LncRNA expression data. Description of data: LncRNA expression data and corresponding AML subtypes. (CSV 8427 kb

Additional file 5: of Expression levels of long non-coding RNAs are prognostic for AML outcome

Supplementary methods. Description of data: Detailed description of the methods used in the analysis. (DOCX 66 kb

Additional file 2: of Expression levels of long non-coding RNAs are prognostic for AML outcome

List of lncRNAs. Description of data: A list of lncRNAs selected using random-forest method. (XLSX 5 kb

Additional file 1: of Expression levels of long non-coding RNAs are prognostic for AML outcome

Supplementary figures and tables. Description of data: Figures and tables. (PDF 2723 kb

Additional file 8: of Expression levels of long non-coding RNAs are prognostic for AML outcome

lncRNA in de novo vs. non-de novo AML. Description of data: Differentially expressed lncRNA in de novo vs. non-de novo AML patients. (XLSX 13 kb

Additional file 4: of Expression levels of long non-coding RNAs are prognostic for AML outcome

List of genes. Description of data: A list of differentially expressed genes in lncRNA subtypes. (XLSX 2264 kb