Bulk Short-Read RNA-seq Library Preparation Services

In collaboration with the UWBC DNA Sequencing Facility and Bioinformatics Resource Core, the Gene Expression Center offers RNA library preparation services for sequencing on the Illumina NovaSeq X Plus or NextSeq platform and data analysis services to meet all your needs under one roof.

We offer the following Bulk RNA library preparation services:

NEBNext Ultra II Directional RNA Library

QIAseq miRNA Library Kit

TruSeq Stranded Total & mRNA (legacy projects)

  • Stranded mRNA: polyA+ enrichment
  • Stranded total RNA: Ribosomal RNA depletion.  (H/M/R (“Gold”); Plant)
  • Ribo-Zero Plus (H/M/R; B. subtilis/E. coli rRNA; globin reduction) Ribosomal RNA depletion. Compatibility with additional species possible with custom probes.

TaKaRa Bio




We provide RNA library preparation services for a variety of RNA sample types (total RNA, reduced rRNA, small RNA, Ip RNA, and mRNA). We use a variety of commercial kits to prepare RNA libraries that have been tested in-house on multiple sample types.

For new clients we recommend a meeting is  scheduled with us to discuss your project before submission.

RNA quality recommendations:

  1. RNA samples should be DNase treated.
  2. A260/A280 ratio range 1.8 – 2.1; A260/A230 ratio should be similar indicating pure nucleic acids.  Inaccurate ratios may also be encountered at very low concentrations (< 10 ng/µl) of nucleic acids.
  3. We strongly recommend the absorbance spectrum of each RNA sample is visually checked to ensure the peak is directly over 260nm.  Residual chemical contamination from nucleic acid extraction procedures may result in an overestimation of the nucleic acid concentration and/or negatively influence downstream analysis.
  4. RNA concentration should be 30-300ng/uL; if >300ng/uL please dilute.
  5. RNA with concentration < 10ng/uL, sample should be quantified on a fluorometer for a more accurate concentration.
  6. Agilent RINe > 7.0.  The RNA Integrity Number (RINe) algorithm is based on a mathematical model that calculates an object quantitative measurement of RNA degradation. RINe represents the relative ratio of the signal in the fast zone to the 18S peak signal. Highest quality RNA is assigned a RINe value of 10. Calculated automatically by the 2200 TapeStation software, RINe provides an objective and reliable numerical assessment of the integrity of eukaryotic/prokaryotic total RNA degradation.

RNA INPUT range per library prep type:

NEBNext Ultra II Directional RNA  25-1,000ng total RNA* (includes both mRNA & rRNA reduction)

TruSeq Stranded RNA 100-1,000ng total RNA* (includes both mRNA & rRNA reduction)

Takara SMARTer Stranded Total RNA Seq v2 Pico Input Mammalian  1-10ng total RNA *

QIASeq miRNA  cells/tissue 1-500ng total RNA (100ng optimal); serum/plasma 5uL from 200uL  serum/plasama extraction (miRNeasy Serum/Plasma Kit or miRNeasy Serum/Plasma Advanced Kit); exosomes 5uL from 1mL serrum/plasma extraction (exoRNeasy Kit )

*when possible we prefer to target a higher INPUT to minimize the number of PCR cycles needed to ensure sufficient yeilds for sequencing


  • Sample IDs must be alphanumeric with 3-20 characters. Dashes (-) are allowed.  No spaces or duplication of names.
  • RNA projects with ≥16 samples, samples must be submitted in a sealed -80C thermostable clear full or semi skirted v-bottom 96-well plate. Plates must be labeled with
  1. Submission Number generated with the service request (M00xxxx)
  2. PI name
  3. Date

A $75 service charge will be incurred for incomplete plate labeling.  Plates filled by row (A1-A12, etc.,) will not be accepted & returned to client at a charge of  $150.

  • RNA projects with <16 samples, samples may be submitted in a 1.5mL tube with the sample ID on the lid and PI name and date on the side. Failure to follow this will result in a $75 service charge.  The sample ID on the lid must match the Sample Submission sheet.
  • We require a minimum of 15uL per sample as 3-4uL is used for RNA QC. If the RNA is suspended in something other than nuclease-free water, please include an aliquot when submitting your samples.
  • QC of RNA will occur within 1-3 business days.  QC will be by NanoDrop and Agilent to confirm conc./purity and integrity, respectively.  Results will be returned to client with comments/suggestions.
  • Remaining template may be returned to client upon request.
  • RNA will be discarded six months post project completion.


The UWBC Bioinformatics Resource Center offers fee for service data analysis options.


A visible measure of a core’s impact is made through proper acknowledgement of usage in abstracts/talks/publications. To acknowledge our core, please use the following statement:

The author(s) utilized the University of Wisconsin – Madison Biotechnology Center’s Gene Expression Center (Research Resource Identifier – RRID:SCR_017757) for RNA library preparation.

UW System Rate

External Rate

Bulk Library Prep Options Details LT (1-48) Samples HT (49-96) Samples LT (1-48) Samples HT (49-96) Samples
NEBNext Ultra II Directional Setup Labor & Ancillary Costs $1,700 $1,900 $2,644 $2,955
NEBNext Ultra II Directional mRNA Per Sample $75 $75 $86.25



NEBNext Ultra II Directional rRNA Removal (QIAseq Fast Select (HMR & Plant) Per Sample $125 $125 $143.75 $143.75
NEBNext Ultra II Directional rRNA Removal (QIAseq Fast Select (-5S/16S/23S) Per Sample $130 $130 $149.50 $149.50
TruSeq Stranded RNA Setup Labor & Ancillary Costs $2,050 $2,375 $3,188 $3,693
TruSeq Stranded mRNA Per Sample $115 $115 $132 $132
TruSeq Stranded Total RNA (Gold) H/M/R Per Sample $180 $180 $207 $207
Ribo-Zero plus rRNA* Depletion Stranded Total RNA Per Sample $225 $225 $259 $259
*Additional custom probes may be needed for efficient rRNA reduction.  The following link may be used to determine compatibility for RiboZero products. https://sapac.illumina.com/products/selection-tools/truseq-total-rna-species-compatibility.html
Illumina RNA Prep, Tagmentation (L) with Enrichment Setup Labor & Ancillary Costs $2,300 $2,300 $3,577 $3,577
RNA Prep, Tagmentation (L) with Enrichment^ Per Sample Contact GEC for Quote
^16 or 96 sample kits contain library reagents to prepare and enrich in 3-plex format.  Indexes and oligo panels NOT included.
Qiagen QIAseq miRNA Setup Labor & Ancillary Costs $1,825 Not available $2,838
Qiaseq miRNA (with UDIs) Per Sample $160 $160 $184 $184
Takara SMARTer v4 / NexteraXT Setup Labor & Ancillary Costs $1,850 $2,190 $2,877 $3,406
Takara SMARTer v4** / NexteraXT Per Sample $150 $150 $173 $173
** Additional Agilent HS DNA chip required for calculation INPUT into NexteraXT assay
Agilent HS DNA chip 1-11 samples $110 $127
Takara SMARTer Stranded RNA v2 Pico Setup Labor & Ancillary Costs $1,875 $2,080 $2,916 $3,235
Takara SMARTer Stranded RNA v2 Pico Per Sample $100 $100 $115 $115
Per Sample include reagents, consumables and final QC costs.

To ensure you are receiving the most up-to-date pricing information, please contact us at gecinfo@biotech.wisc.edu to request a quote. Thank you!

All data and services provided by the University of Wisconsin Biotechnology Center Gene Expression Center are intended for research purposes only. Services are not intended nor certified for diagnostic or clinical use.