Library construction is the process of taking DNA, RNA or other nucleic acid material from its "native" state to a form that can be run on the Illumina sequencer. The majority of protocols require fragmentation of the nucleic acid material to a specific size range. The BPF offers shearing services using the Covaris S2 instrument. There are dozens of methods and kits for the production of Illumina compatible libraries available as well as multiple automation platforms to run these methods. The BPF has adopted the Apollo Wafergen 324. We offer a variety of library methods on this instrument. Please see the Service Description section below for a complete list of methods currently available from our core.

Library Preparation

Our facility offers library preparation services starting with purified DNA or RNA. We are able to make libraries for a variety of application types, see table below. Additional procedures, upstream from basic library preparation, are the responsibility of your laboratory. For example, our facility does not provide chromatin-immunoprecipitation services but we do offer construction of ChIP-Seq libraries from the point of isolated, purified ChIP DNA. If you are interested in a library prep service and do not see it below, please contact us. We are always happy to discuss options not yet listed!.

Starting Material Material Sub Type General Application Category BPF Service Name Kit / Procedure Available
DNA Amplicon Genomic-Seq Genomic-Seq Wafergen PrepX DNA Wafergen Yes
DNA cDNA RNA-Seq Genomic-Seq Wafergen PrepX DNA Wafergen Yes
DNA ChIP ChIP-Seq ChIP-Seq Wafergen Chip-Seq Wafergen Yes
DNA Genomic Genomic-Seq Genomic-Seq Wafergen PrepX DNA Wafergen Yes
DNA Genomic Nextera Nextera XT Nextera XT Yes
RNA Total RNA RNA-Seq Total RNA-Seq Wafergen Takara Ultra Low v4 and Nextera Yes
RNA mRNA RNA-Seq Directional RNA-Seq Wafergen Directional RNA-Seq Wafergen Yes
RNA Ribosomally Reduced RNA RNA-Seq Directional RNA-Seq Wafergen Directional RNA-Seq Wafergen Yes
  • Apollo Wafergen 324 Robot
  • Covaris S2
  • MJ Research Tetrad DNA Engine Thermal Cycler
  • Qiagen Qiagility Robot

Please provide starting material as specified in the table below. If you are not able to determine the quantity or quality of your starting material, you should order Bioanalyzer or TapeStation services prior to ordering your library prep service.

BPF Service Name Material Provided to BPF # of Indices Available* Minimum Input Material Amount ** Maximum Input Material Amount OD 260 / 280 RIN Volume µL (Sheerd / Unsheared ) Notes
Genomic-Seq Wafergen Amplicon DNA 24 1 ng 3 µg ~1.8 15 / 100 Size of amplicon DNA should be within library size and read length limits of the Illumina HISeq or MiSeq.
Genomic-Seq Wafergen cDNA 24 1 ng 3 µg ~1.8 15 / 100 cDNA must be sheared to proper size range prior to library construction. Shearing service is available.
ChIP-Seq Wafergen ChIP DNA 24 1 ng 3 µg ~1.8 N/A / 15 Size of ChIP DNA should be within library size and read length limits of the Illumina HISeq or MiSeq. It is not recommended to shear ChIP DNA post IP.
Genomic-Seq Wafergen Genomic DNA 24 1 ng 3 µg ~1.8 100 / 100 Genomic DNA must be sheared to proper size range prior to library construction. This service is available.
Total RNA-Seq Wafergen-Low Input Total RNA 96 20 ng 200 ng ~2.0 >8 N/A / 5 This method uses Takara UltraLow V4 amplification to amplify non-repetitive RNA and conversion to cDNA. (Eukaryotes Only)
Directional RNA-Seq Wafergen Total RNA 24 200 ng 1 µg ~2.0 >8 N/A / 20 Additional fee for Ribosomal reduction(Human, mouse, Rat-other organisms kit must be provided) or mRNA isolation using oligo dT beads
Directional RNA-Seq Wafergen Ribosomal Reduced RNA 24 1 ng 100 ng ~2.0 >8 N/A / 10
Directional RNA-Seq Wafergen mRNA 24 1 ng 100 ng ~2.0 >8 N/A / 10
Nextera XT Genomic DNA 96 1 ng 5 ng ~1.8 N/A / 5 DNA must be quantified by Bioanalyzer, Tape Station, or Qubit. Submit samples at 0.2 ng/µl, in sets of 12, for 96 samples at once. Samples will have dual indexing strategy.
* The BPF Stocks 24 Illumina compatable adapters with indices for use in all Wafergen methods. More adapters are available. If you project requires > 24 indices, please contact our staff.
** Assumes material is proper size range. If shearing, 500 ng is needed.
Service
Harvard Internal
Harvard Affiliate/Academic
Commercial
Setup Fee* Per Sample Setup Fee* Per Sample Setup Fee* Per Sample
ChIP-Seq Wafergen Bead X High $97.28 $82.74 $111.87 $95.15 $126.46 $107.56
Covaris Shearing $135.35 $71.25 $155.65 $81.94 $175.95 $92.63
DNA-Seq Wafergen Prep X $90.62 $110.74 $104.21 $127.35 $117.80 $143.96
Nextera DNA normalization $6.03 $2.68 $6.93 $3.08 $7.84 $3.49
Nextera Illumina Nextera XT2 $163.69 $46.74 $188.25 $53.75 $212.80 $60.76
Nextera Illumina Nextera XT2 - C1 $167.33 $13.29 $192.43 $15.28 $217.53 $17.28
QC DNA Dilution $0.00 $6.95 $0.00 $7.99 $0.00 $9.04
RNA-Seq Wafergen RNA-Seq (Directional) $150.21 $160.56 $172.74 $184.64 $195.27 $208.73
RNA-Seq Wafergen RNA-Seq (Directional) (9 - 48) $164.87 $124.14 $189.60 $142.77 $214.33 $161.39
Ribosomal Reduction $157.53 $90.62 $181.16 $104.21 $204.79 $117.80
mRNA Isolation $88.50 $51.04 $101.78 $58.69 $115.05 $66.35
smRNA-Seq Qiagen smRNA-Seq $202.11 $104.70 $232.42 $120.41 $262.74 $136.11
Illumina Nextera XT2 Library Prep - No Sample Fee $46.40 $53.36 $60.32
* Setup Fee is for each batch of 1 to 8 samples
** Total RNA-Seq Wafergen-Low Input combines SPIA, Covaris Shearing, and DNA-Seq Wafergen Prep X.

Although we provide copies of Illumina's protocols, we recommend you check the Illumina or other vendor's web sites to obtain the latest version of any given protocol.

Every library we produce is run on an Agilent 2100 Bioanalyzer Hi-sensitivity DNA chip or an Agilent 2200 TapeStation D1000 HS ScreenTape to assess concentration and size distribution of the library molecules. In addition, a QPCR assay is run to determine functional concentration of the final library in an effort to obtain optimal cluster densities prior to the sequencing process.

Quality Control services have a small additional fee. Further information regarding this service can be found in out NextGen Sequencing section.