At the GRCF High Throughput Sequencing Center, our goal is to provide the research community at Johns Hopkins University with access to ‘next generation’ sequencing platforms. We currently feature three HiSeq 2500 instruments and two MiSeq instruments, and an Ion Proton (currently in R&D).  We do our best to sequence samples in a timely manner, but our first priority is high quality data.

We offer simple, per lane pricing, along with end to end service for whole exome/custom targeted projects, RNASeq, and whole genome.

We offer free consultation. Please contact David Mohr to discuss your project in detail.

Per Lane Pricing (Rapid Mode)

Single Reads:Paired End Reads:
50 bp: $1,200 per lane50 bp (x2): $1,900 per lane
100 bp: $1,600 per lane100 bp (x2): $2,400 per lane
150 bp: $2,000 per lane150 bp (x2): $2,900 per lane

Non-standard read lengths are also available, provided they are submitted in pairs (enough to start a 2500 run). Please inquire about pricing.

High Output Runs are available, but you will need to submit a full flowcell (ie. 8 lanes/libraries) at a time.  Please inquire for pricing.

Sample Requirements

Completed Libraries: Please submit 10μl of your sample at 2nM.  Samples must be pooled.  We will do a QC check via Bioanalyzer to increase the likelihood of quality data, but you should quantitate your sample as accurately as possible.  Nanodrop is not reliable.  qPCR is by far the most accurate, but intercalating dye methods can be used.

Library Prep:  $250/sample.  Please provide us with >500ng of high molecular weight DNA/RNA.  Please contact us to discuss sample submission.

Data Yield

Our facility features the HiSeq 2500 platform. We almost exclusively run our instruments in Rapid Run Mode, due to the fast run times and low error rates. Yield is dependent upon several factors:

  • Read Length: the longer the read, the more data.
  • Read Type: paired end reads yield twice the data as single read.
  • Optimal Cluster density: it is imperative to accurately quantitate your library to ensure high data yield. We do our best to QC libraries before sequencing, but we cannot pool samples for you.
  • High Quality Library: libraries that contain a high level of adapter dimers will yield significantly less data, as the fragments will hybridize to the flowcell. Similarly, over amplified libraries can negatively impact yield.
  • Uniform Base composition: while less of an issue than in the past, libraries that have uneven base composition tend to pose problems with the HiSeq analysis software. These issues can be mitigated using several strategies, but the net effect will be lower data yield per lane than a balanced library.

Please see Illumina’s HiSeq 2500 Specification page for current data yields. While we regularly achieve greater than ‘spec’ yields from the HiSeq2500, typicially matching yields for High Output mode, it is best to be conservative when planning your experiments.

Data Delivery

Per lane sequencing:  Data will be returned in Sanger FASTQ format via our high speed aspera server

End to end services:  alignment files, variant calls, and any intermediate files you wish via aspera server

 

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