BioMicroCenter:FAQ

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'''PHONE:''' The main lab number is 617-715-4533 <BR>
'''PHONE:''' The main lab number is 617-715-4533 <BR>
Our director, [[User:Stuart S. Levine|Stuart Levine]], can be reached at 617-452-2949.
Our director, [[User:Stuart S. Levine|Stuart Levine]], can be reached at 617-452-2949.
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== HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED ==
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This is a very hard question to answer because it involves a number of variables. The simplest answer is, samples preparation typically takes ~1-2 weeks for standard samples with all reagents on hand. For newer or rarely used methods, the number can extend to a month if we need to gather reagents. Once the sample is ready, it goes in to the sequencing queue. This queue is often the longest part of the process. Once the full flowcell is ready and put on a sequencer, it takes ~1.3h per base to sequence (this used to be 1h but upgrades to the machines have slowed them down some). A 40nt read takes just over 2 days. Turn around (for PE samples) functionally takes about a 1/2 day. So a 100+100PE sample will take about 11 days once it is on the sequencer - if nothing goes wrong.
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GAII and MISEQ are much simpler. Once the sample is prepped and the machine is working, it will be loaded immediately. Total times should be less than 3 weeks.
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=== Illumina Queue: Full Flowcells ===
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The primary requirement for a run is a full flowcell.
== HOW DO I GET MY DATA ==
== HOW DO I GET MY DATA ==

Revision as of 10:28, 27 August 2012

Image:BioMicroCenter-header6.jpg

Contents

CONTACT

STOP BY: The BioMicro Center is located at 68-316 on the MIT campus.
EMAIL: The BioMicro staff can be emailed at biomicro@mit.edu
PHONE: The main lab number is 617-715-4533
Our director, Stuart Levine, can be reached at 617-452-2949.

HOW LONG WILL IT TAKE FOR MY HISEQ SAMPLE TO BE SEQUENCED

This is a very hard question to answer because it involves a number of variables. The simplest answer is, samples preparation typically takes ~1-2 weeks for standard samples with all reagents on hand. For newer or rarely used methods, the number can extend to a month if we need to gather reagents. Once the sample is ready, it goes in to the sequencing queue. This queue is often the longest part of the process. Once the full flowcell is ready and put on a sequencer, it takes ~1.3h per base to sequence (this used to be 1h but upgrades to the machines have slowed them down some). A 40nt read takes just over 2 days. Turn around (for PE samples) functionally takes about a 1/2 day. So a 100+100PE sample will take about 11 days once it is on the sequencer - if nothing goes wrong.

GAII and MISEQ are much simpler. Once the sample is prepped and the machine is working, it will be loaded immediately. Total times should be less than 3 weeks.

Illumina Queue: Full Flowcells

The primary requirement for a run is a full flowcell.

HOW DO I GET MY DATA

You will be notified by email that your data is ready. The data will be placed on one of our server for you the download.

Windows

Macintosh Application

UNIX

  • Samples can be copied from our servers using scp
  • Use the SSH client or Fetch to find the precise filenames / directory you want.

Direct Mount

Illumina data is also made available by direct mount for many users on the MIT campus or who are running VPN. While we are transitioning to the Isilon system, not all labs may have access. Contact Stephen Goldman if you are interested.

Accessing the server

Your user name and password will be included in the email. To obtain your data, enter the following in your client:

 Host:       bmc-150.mit.edu
 user:       provided in email      
 Password:   provided in email

Please contact Stephen Goldman if you have difficulty obtaining your data.

NON MIT USERS

Do you take samples from outside MIT?

The BioMicro Center is built to serve the MIT community. As such, members of the MIT community have priority on all of our services. However, if we have extra capacity, we are happy to make it available scientists not affiliated with MIT, with the caveats that MIT samples *always* have priority and that access is finite. The BioMicro Center retains the right to refuse any sample.

How can we ship samples to you?

Please email biomicro@mit.edu to arrange a drop off date and time. DNA samples should be shipped at 4C and RNA samples should be shipped on dry ice.Samples should be submitted with a completed order form and shipped by overnight delivery to:

 MIT BioMicro Center
 31 Ames Street, Building 68-316
 Cambridge, MA 02139

The pricing form says "NA". What does that mean?

Some of our services are specifically restricted to the MIT community and we cannot offer them to outside users. Others are restricted to academic labs. Please email us at biomicro@mit.edu if you have any questions.

What is your billing address?

Payments should be made to our finance office at:

 Massachusetts Institute of Technology
 Biology Finance Office, Attn: Alison Salie
 77 Massachusetts Avenue, 68-157
 Cambridge, MA 02139
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