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Table 1 Summary of RNA-Seq Data sets used in this study.

From: Bias detection and correction in RNA-Sequencing data

Data Set Source Accession Number Technology Characteristics Notes References
MAQC data set Sequence Read Archive SRX016366, SRX016368-SRX016372 Standard Illumina RNA-Seq protocol: RNA fragmentation, random hexamer priming expression data also available from Taqman RT-PCR and QuantiGene platforms [22]
RNA-Seq data from kidney and liver Sequence Read Archive SRX000571 SRX000605 Standard Illumina RNA-Seq protocol: RNA fragmentation, random hexamer priming read counts per gene available from http://bioinf.wehi.edu.au/resources/ [7]
Yeast RNA-Seq data Sequence Read Archive SRR014335 SRR014336 Standard Illumina RNA-Seq protocol: RNA fragmentation, random hexamer priming NA [25]
Yeast RNA-Seq data using alternative protocols Sequence Read Archive SRR002058
SRR002062
random hexamer or oligo-dT priming; cDNA fragmentation by DNase I NA [26]
FRT-Seq data European Nucleotide Archive ERR007689
ERR007710
standard protocol or FRT-Seq (no PCR, RT step on flow cell) read counts per gene available from ftp://ftp.sanger.ac.uk/pub/transseq/ [27]