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).
Illumina libraries (ab, bc, and ac) were prepared according to the Illumina paired-end sample preparation guide with the following modifications.
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).
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).
Total RNA samples were prepared for smRNA sequencing using Illumina's Small RNA v1.5 Sample Preparation Guide.
