From Genome Technology Core (GTC) wiki - Sequencing and Microarray
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Prices quoted are for Whitehead Institute/MIT only. In order to cover additional costs associated with providing outside service, non-WI/MIT institutions should add 30% to the list price.

Illumina Sequencing

There are two options for Illumina sequencing. HiSeq "Standard" and HiSeq "Rapid".

Prices include basic data processing including base calls, quality scores and alignment (if requested).

Please visit the Sequencing Services page for sample submission instructions and more information about library prep services.

HiSeq (Std a.k.a. "High Output" mode) -- At least 150-200 million reads per lane

Standard mode require 7 full lanes of samples before sequencing can proceed and takes about 1 day for every 25 bases of read length. Note: You do not need to fill out a full flow cell yourself, we will group you with other samples to fill out a run.

Item Unit Price Per Unit Notes
HiSeq - 50 bp Single Read Lane $1,200
HiSeq - 28x40 10X Lane $1,500 ONLY FOR 10X LIBRARIES
HiSeq - 60x60 Paired End Lane $1,750
HiSeq - 100x100 Paired End Lane $2,250
HiSeq - Additional 70 bases Lane $400 Add to above base prices for longer reads

HiSeq (Rapid) -- At least 100 to 150 million reads per lane (Two lanes per Flow Cell)

In "Rapid" mode, individual samples can be sequenced much more quickly without the need to fill out full flow cells. Read lengths in Rapid mode are also longer, up to 250x250, and complete more quickly. For example - a 100x100 run in Rapid mode completes in 2-3 days vs up to 7 days in Standard mode.

Item Unit Price Per Unit Notes
HiSeqRapid - 50 bp Single Read full flowcell (2 lanes) $2,300
HiSeqRapid - 28x40 10X full flowcell (2 lanes) $2,800 ONLY FOR 10X LIBRARIES
HiSeqRapid - 60x60 Paired End full flowcell (2 lanes) $3,400
HiSeqRapid - 100x100 Paired End full flowcell (2 lanes) $4,350
HiSeqRapid - 250x250 Paired End full flowcell (2 lanes) $7,200
HiSeqRapid - Add DUAL mode full flowcell (2 lanes) $460 ONLY required if running different samples in each lane
HiSeqRapid - Additional 70 bases full flowcell (2 lanes) $560 Add to above base prices for longer reads up to 250x250

Library Prep

Item Unit Price Per Unit Notes
Swift ChIP DNA (ChIP-Seq) Sample $200 Optimized for low input ChIP
TruSeq Nano gDNA (Genomic) Sample $200 Genomic DNA >100ng
Nextera gDNA (Genomic, ATAC-Seq) Sample $200 "Tagmentation" prep from intact gDNA (50ng)
KAPA Hyper Prep - Stranded (RNA-Seq) Sample $200
Clontech UltraLow RNA (RNA-Seq) Sample $300 For low input RNA down to single cell
Clontech Stranded Total RNA Pico (RNA-Seq) Sample $250 -
NEBNext Small RNA (microRNA) Sample $200 -
10X Single Cell 3’ Solution Library prep (RNA-Seq) Sample $2,000 Sorting and library prep for up to 10,000 cells
SMART-seq v2 Library prep (RNA-Seq) 96-well Plate $2,500

Quality Control

Item Unit Price Per Unit Notes
Bioanalyzer Sample $15 Sizing and purity analysis
qPCR Sample $25 Quantification
Sample Multiplexing Sample $10 Mixing samples for multiplex run

nCounter Analysis System (NanoString)

Item Unit Price Per Unit Notes
Reagents Cartridge ---- Reagents and Codesets Purchase From Nanostring
Equipment Use Cartridge $250 12 samples per cartridge
Labor-Hyb Cartridge $150 -
Labor-miRNA Sample $25 Addon for miRNA protocol only

Bioanalyzer - RNA, DNA and Protein analysis

Item Unit Price Per Unit Notes
RNA or DNA Sample $15 Pico, Nano, DNA or hsDNA

Quantitative PCR - QuantStudio 6

Item Unit Price Per Unit Notes
SYBR green / Taq Man Master mix uL 7 cents -
Optical Plate Plate $7 -
Equipment Time (2 hour time block) Plate $30 Sign-up Required