Sample preparation for Illumina-based mRNA sequencing was conducted based upon the manufacturer's protocols "mRNA Sequencing Sample Preparation Guide" and "Preparing Samples for Multiplexed Paired-End Sequencing" (Part# 1005361Rev B, and Part# 1004898Rev D, Illumina, Inc., San Diego, CA).
The Illumina TruSeq™ RNA Sample Preparation Guide was followed to prepare the samples for sequencing.
Libraries were prepared following the TruSeq RNA Sample Preparation Guide (Illumina).
Paired-end libraries were prepared according to the TruSeq™ RNA Sample Preparation Guide (Illumina).
The manufacturer's mRNA sequencing sample preparation guide (Illumina, Inc., San Diego, CA) was used to prepare two pools of total RNA for paired-end sequencing (101 bp read length).
Illumina libraries (ab, bc, and ac) were prepared according to the Illumina paired-end sample preparation guide with the following modifications.
The PE reads were 100 bp, while the 2 Kb MP reads were 45 bp. 3 Kb and 5 Kb MP libraries were prepared according to "Mate Pair Library v2 Sample Preparation Guide" [ 26] at Aarhus University (Denmark).
The workflow in the Nextera Enrichment Sample Preparation Guide (Revision B) by Illumina was followed to prepare the libraries for whole-exome sequencing.
For genomic DNA, a paired-end library was prepared according to the manufacturer's paired-end sample preparation guide (Illumina, San Diego, CA, USA) and run on an Illumina HiSeq™ 2500 sequencer (Illumina, San Diego, CA, USA) by Ambry Genetics (Aliso Viejo, CA, USA).
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