MBCF: Genomics

Molecular Biology Core Facilities: Genomics Core Services

Illumina MiSeq Sequencing

~16M reads

Run Programs

• 1 X 50bp, 600-800 Mb
• 2 X 30bp, 720-960 Mb 
• 2 X 150bp, 3.6-4.8 Gb 
• 2 X 250bp, 6.0-8.0 Gb

MiSeq Pipeline

Consultation
If it is your first time running MiSeq samples at the MBCF or you have something new that you would like to try please Contact Us for a brief consultation. 

DNA Library Considerations and Requirements
The library should consist of DNA fragments that are between 200-800bp with Illumina PE adapter sequences. For optimal clustering and basecalling it helps to have a relatively narrow size range (~200bp). Even if you are only running single-end sequencing, the MiSeq requires PE adapters for cluster generation. Libaries prepped for HiSeq or GAII single end runs may NOT be compatible with the MiSeq. Libraries with low base diversity are also problematic and can require phiX spike-in of 30%-60%, or an alternative library construction approach for successful clustering and sequencing. Email to ask about our Nextera Library Prep Service

DNA Library QC

MBCF will spec samples on Qubit fluormeter to determine concentration of dsDNA and analyze on a TapeStation for fragment size information to estimate library molarity and to determine appropriate loading amount for optimal cluster generation. qPCR will be available soon as well.

Sequencing
Actual run times vary from 4hrs to 40hrs depending on the number of cycles requested. Our turnaround time is usually within 2-3 days of receiving the sample and sometimes as fast as same day for shorter runs.

Data Transfer
Upon run completion fast will be made available on our webserver along with instructions for access. You may request an Illumina BaseSpace link to you. We can also provide data alignment to a reference sequence (this should be addressed during the consultation)

Nextera Illumina Library prep

MBCF Genomics Instrumentation

3 Illumina MiSeqs (Single Lane NGS)

Agilent TapeStation (DNA size analysis)

Sage Science Pippin Prep (DNA Size Selection)

Qubit Fluorometer

Sample Drop-off Locations

Samples can be dropped off in the MBCF Fish room near 3rd floor elevator lobby of Smith, directly to our lab on the 4th floor of DFCI Fenway Campus, or shipped via FedEx. 

Physical Street Address / Fedex Delivery:
Molecular Biology Core Facilities
Dana Farber Cancer Institute North Campus
21-27 Burlington Avenue 4th Floor
Boston, MA 02215
USA

US postal, UPS, Mailing Address:
Molecular Biology Core Facilities
Dana Farber Cancer Institute North Campus
450 Brookline Avenue, BA404
Boston, MA 02215
USA

Information for Users External to DFCI

Purchase Orders are to be made out to:

Dana Farber Cancer Institute

General Accounting, BP-425

450 Brookline Avenue

Boston, MA 02215-5450

Note to Partners, Harvard, Boston Children’s and Tufts researchers:

• Partners Health Care (includes MGH, BWH, McLean, Spaulding, etc): choose vendor 0000008573
• Harvard (includes HMS,Dental, Wyss, HSPH, etc.): choose vendor site: 01_PRIMARY
• Tufts University: choose Supplier 0000000655
• Boston Children’s Hospital: choose vendor 0000001886

 If you are using a PO from an institution other than one under which you signed in, you must stop and contact the DFCI iLab staff at sc_billing@dfci.harvard.edu

Contacts

Map

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Click on this map for specific directions to and from Logan Airport and the Mass Pike as well as a good place to eat while visiting MBCF.