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Pricing for Illumina HiSeq 2000 mRNA-Seq Sequencing Services

Illumina HiSeq 2000 mRNA Seq Sequencing Services

Microarray Core Facility
Huntsman Cancer Institute Room 3350
2000 Circle of Hope
University of Utah
Salt Lake City, UT 84112
801-585-7192 (office)
801-581-6346 (lab)

Illumina HiSeq 2000 Sequencing Services performed at the HCI Microarray Core Facility are partially supported by NCI Cancer Support Grant P30CA042014 and by institutional support provided through the Huntsman Cancer Institute.

Pricing for mRNA Seq Sequencing Services

Service Category


Pricing Unit

University of Utah Pricing

External Pricing

Sample QC QC Total RNA per sample $8.00 $12.00
Library Preparation mRNA-Seq Library Prep per sample $180.00 $270.00
Illumina Sequencing HiSeq2000 50 Cycle Single Read Sequencing per lane $800.00 $1200.00
Library QC Post-Library Quality Control per library $20.00 $30.00
Option 1 Epicentre RiboZero Treatment per sample $80.00 $120.00
Illumina Sequencing HiSeq2000 101 Cycle Paired End Sequencing per lane $1800.00 $2700.00
  • All total RNA samples submitted to the core facility for library construction will go through quality control (NanoDrop spectrophotometer reading and quality evaluation on an Agilent Bioanalyzer RNA 6000 chip) prior to library construction.
  • Barcode: All libraries constructed at the core facility will include an index barcode tag which enables multiplex sequencing if desired. qPCR is performed on all samples prior to combining indexed samples that will be run in the same lane to provide a more accurate concentration of cluster forming units in the library. Although the intention of qPCR is to equalize the molarity of all samples that contribute to a single lane, it is not perfect and one should expect that at times there will be up to a 20% deviation in the sample that is most highly represented and the one that is most lowly represented.
  • The mRNA fraction of total RNA is captured by oligo-dT magnetic beads and the mRNA is subsequently randomly fragmented as the first steps of library construction. The average insert size for mRNA-seq libraries ranges from approximately 100-400 bp. Capture of mRNA with oligo-dT beads is included as part of the standard library construction price.
  • As an alternative to oligo-dT capture of mRNA, we also offer an optional service of removal of rRNA using the Epicentre RiboZero kit. Epicentre has separate offerings for Human/mouse/rat and for Gram positive bacteria and for Gram negative bacteria. There is an additional charge for this service and this is not part of the standard library preparation process.
  • Post-Library Quality Control includes the following services: (1)NanoDrop reading, (2)Q-pcr quantitation of library concentration using Illumina primers, and (3) evaluation of library on a Agilent Bioanalyzer DNA 1000 chip. These services are included with the pricing for library construction when the library is constructed at the core facility. If the library has already been constructed when submitted to the core facility, a post-library quality control charge will be added to the charges for the sequencing.
  • Most mRNA-Seq libraries are sequenced on a 50 cycle Single End Read sequencing run.
  • Version 3 flowcells are currently used for single end and paired end read sequencing and these have a specification of delivering 150 to 200 million passed filter reads per lane. Illumina's specification is based on samples that have previously been run at least one time since this allows you to optimize the cluster number on future runs. We attempt to meet this specification on the first run for each lane of samples.
  • Another option for sequencing of mRNA-Seq libraries is a 50 cycle Paired End sequencing run. However, this facility runs few flowcells of this run type and it may necessitate that you provide samples for all eight lanes of the flowcell in order to have libraries run on a 50 cycle paired end run. We do routinely run 101 cycle paired end sequencing flowcells and the pricing for this option has been provided above.
  • Illumina sequencing flowcells contain eight lanes and all eight lanes must be filled prior to starting the sequence run. Most sequencing runs contain samples from multiple clients. However, we do not mix barcoded samples from different clients into a shared lane on the same flowcell.
  • A PhiX control library that is constructed by Illumina is spiked into each lane at a concentration that represents approximately 0.5% of the reads.