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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]