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The DNA Resource Core offers the following sequencing services

  • Large (48 or more samples) and small-scale (<48 samples) DNA sequencing projects.

    The turn-around time for next-day sequencing reactions is 24 hours, with sequence reads and quality reports posted on a secure website for users to download and analyze.

  • Same-day sequencing

    Our turn-around time for same-day sequencing is eight hours or less from sample arrival to data retrieval. This service is now available to users who drop off at the three locations of Harvard Medical School campus and the cold room of the Biolabs building (16 Divinity Ave) in Cambridge, MA before 9am. Samples for same-day results submitted between 9am and 10am should be delivered directly to the Core at Building C2. Room 204, 240 Longwood Ave. Boston, MA 02115.

  • Automated, high-throughput plasmid DNA preparations

    Our equipment can process several 96-well plates from glycerol stock to bacteria pellets to DNA's for sequencing reactions with a reasonable turn-around time. If you're planning a large project that involves plasmid preps and sequencing, please contact Li Chan to talk about planning and pricing.

  • No charge for reruns

    We offer free reruns for failed sequencing reactions to test for potential sequencing problems originating at the facility.

 

Free Software Downloads

DNA Sequencing Sample Preparation

Overview


STEP ONE

labelling samples with order number and marking which the first sample is

Label your samples with the five-digit order number obtained after submitting the sequening request online. Please mark "T" for template and "P" for primer, and also mark "1" on the first sample so that we know the orientation of your order.

STEP TWO

arraying samples

Array your templates and primers in 96-well plates for large orders only. For small orders cut the 96-well plate to fit your number of samples. PCR strip tubes may also be used.

STEP THREE

Seal plates with foil seals provided at drop-off locations and be sure seals adhere well so samples don't evaporate or spill to different wells.

STEP FOUR

centrifuge sample plate

Please centrifuge the samples before dropping off.


Step-by-Step Sample Prep

 

Sample Submission
Prepare Your Template DNA Template DNA should be prepared as high-quality plasmid DNA or purified PCR product DNA. (Alternatively, you can submit plasmids as glycerol stocks and we will prep the DNA for you in advance of sequencing. Please contact Li Chan for more information.
Array Your Samples Samples should be arrayed on non-skirted, 96-well plates and sealed with aluminum adhesive seals. Plates and seals can be found at drop-off locations. Samples should be organized as shown in the figure below (1 to 96 numbering). Please be sure to label the plate (rather than the foil seal).  Please note - you can cut the plate if you're submitting a partial plate of samples and use the rest of the plate another time. We would like to avoid wasting a whole 96-well plate for, say, just 8 samples.
Array Your Primers Please submit your primers on a SEPARATE PLATE, arrayed in the same format as your DNA templates (so that we can simply pipet one into the other with a multi-channel pipet or robotic pipet system). Please be sure to label the plate (rather than the foil seal). Standard primers (table below) are provided by the Core at no additional charge -- please indicate on your order form if you would like us to add primer at the facility. Again, please cut the plate and save the remainder to use at another time if you're submitting just a few samples.
Place Your Order Place your order on-line.  Please be sure to add any comments you may have regarding your samples such as High GC content. Please add primers at facility, etc
Submit Samples Submit your samples (templates & primers arrayed on separate plates) by placing them in a drop-off location freezer or sending them to the facility. Alternatively, contact Li Chan to arrange pick-up from MGH, Harvard Square, or another Boston-area location.

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How to Array Samples

Please number your samples as shown in white (top to bottom, left to right, one to ninety-six):

  1 2 3 4 5 6 7 8 9 10 11 12
A 1 9 17 25 33 41 49 57 65 73 81 89
B 2 10 18 26 34 42 50 58 66 74 82 90
C 3 11 19 27 35 43 51 59 67 75 83 91
D 4 12 20 28 36 44 52 60 68 76 84 92
E 5 13 21 29 37 45 53 61 69 77 85 93
F 6 14 22 30 38 46 54 62 70 78 86 94
G 7 15 23 31 39 47 55 63 71 79 87 95
H 8 16 24 32 40 48 56 64 72 80 88 96

Tips for arraying your samples:

  • If you have fewer than 96 samples, please array and number them by vertical column (not by row).  For example, 15 samples should take up column one (#1-8) and part of column two (#9-15) with a blank noted at position 16.
  • If you have only a few columns of samples, please feel free to use 8-sample strips and lids instead of the plates and seals (both will be provided at drop-off locations).
  • Users are only charged for the samples submitted.  The Core no longer charges in columns of eight.

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Template and Primer Concentrations

Please determine the concentration of your purified DNA carefully:  more than 75% of sequence failures can be attributed to incorrect concentrations of template DNA.

For Plasmid DNA
Template Concentration Volume Primer Concentration Volume
100 ng/µL 12 µL per well on the Template Plate 1.6 pmol/µL 12 µL per well on the Primer Plate

For purified PCR products
Template Concentration Volume Primer Concentration Volume
5 ng/µL per 100 bp 12 µL per well on the Template Plate 0.4 pmol/µL 12 µL per well on the Primer Plate


For example, a concentration of 25ng/µL is appropriate for a 500bp PCR product.

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Sequencing Primers

We supply the following primers at no additional charge:

T7 5'-TAATACGACTCACTATAGGG-3'
T7 Terminator 5'-TATGCTAGTTATTGCTCAG-3'
SP6 5'-CATACGATTTAGGTGACACTATAG-3'
M13 Forward 5'-GTAAAACGACGGCCAGT-3'
M13 Reverse 5'-CAGGAAACAGCTATGACC-3'
T3 5'-AAATTAACCCTCACTAAAGG-3'
CMV Forward 5'-CGCAAATGGGCGGTAGGCGTG-3'

Please indicate in the "comment" box on your order form if you would like us to add a primer at the facility.

 

 Prices for DNA Sequencing Services

  48 samples or more
Fewer than 48 samples
Same-Day Sequencing
Plasmid Extraction
DF-HCC Members and Harvard Users $3.00/reaction $4.00/reaction $7.50/reaction $1.50/sample
Other Academics and Nonprofits $3.50/reaction $4.50/reaction $8.50/reaction $2.50/sample
Commercial Users $4.20/reaction $5.40/reaction $9.50/reaction $2.75/sample

For information regarding DF/HCC membership eligibility please visit this page.

If you would like to confirm your PI's membership status you can consult the following list of current DF/HCC members.

We bill only for the samples you submit. If you submit 4 samples you are charged for 4 samples based on the pricing structure of your organization. Special pricing is available for large orders. Please contact the core in these instances.

 

Sequencing Login and Registration

Please login using your email address.

If your password doesn't work, please click the"forgot your login information" link.

If you are a NEW USER here are some things to keep in mind:

  • For Sequencing sign-up, please click on "Create Login Account for dnaLIMS" and follow instructions to create a new account.
  • If your PI is not in our list please contact Li Chan to have them added. Please DO NOT sign-up without verifying your PI info.

 

Longwood and Cambridge Area Drop-Off Locations

  • Pick-ups are on Monday-Friday between 7-9am. Leaving samples at the drop-off location in the evening is the easiest and fastest way for pick-up and for you to get your results.
  • Current turn-around time from receipt of your samples is ~24 hours for next-day sequencing and 8 hours or less for same-day sequencing.

Location of Drop-Off Sites

What you'll find at Drop-off Locations

  • Freezer space where you can leave your samples for pick-up (weekday mornings). Please note that we were only permitted to place a cooler at the 7 Cambridge Center location for sample drop-offs.
  • Supplies such as plates, plate seals and PCR tubes.

Not at HMS or Harvard Square? Please send samples to the DF/HCC DNA Resource Core at 240 Longwood Ave C1-204, Boston, MA 02115 via FedEx or UPS. Please also make sure that samples are sealed tightly with foil seals or caps and wrapped with enough absorbent and cushioning material.


 

Maps You May Find Helpful:

Longwood Medical Area


map of Longwood medical area


HMS Quad


map of Harvard Medical School quad


Harvard Square


map of Harvard Square area

 

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