BioMicroCenter:FAQ

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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 weeks for standard samples with all reagents on hand (QC, prep, QC). 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. Each flowcell is composed of 7 lanes that must be run together. In the BioMicro Center, lanes are grouped by read length to optimize throughput and keep costs low. This requirement for 7 samples has a major impact on queue time. If you do a common read length, such as 40nt SE, the queue length will be short. On the other hand, if you ask for an unusual read length (eg. 100nt SE), your samples may never come off the queue. By frequency, the most common read lengths are, in order: 40SE, 40+40PE, 80+80PE. We do fudge a little in some of the long read lengths to fit samples in (mixing 80+80 and 100+100PE for example), but we will always give priority to the samples of the read length we are going to do. We do not run incomplete flowcells and other options, such as GAII and MiSeq exist for unusual read lengths. NOTE: Barcoding is assumed to be done on all flowcells and we do NOT restrict pooling based on which samples are multiplexed and which are not.

Illumina Queue: Priority

Priority	Type
1	Reruns of failures
2	Samples from labs that bought the equipment
3	MIT CORE labs
4	MIT non-CORE labs
5	non-MIT users

The BioMicro Center queue operates on a tiered priority basis (see table). We hold to this priority schema as closely as we can while still needing to fill flowcells. Some caveats: Once a flowcell is quality controlled and "on deck" for clustering, that flowcell is considered locked and no new submissions will be added to it. Additionally, once a flowcell is clustered, all samples on that flowcell WILL BE BILLED, regardless of if the samples are withdrawn. Clustering can happen a week or more before loading. Once flowcells are clustered, their order is set barring the need for reruns.

Failures

The Illumina HiSeq is an unfortunately temperamental beast.

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

• There is a Windows applications client called SSH Secure Shell available at :
• http://biomicro-bioanalyzer.mit.edu
• Instructions to use the application can be found Instructions to use SSH .

Macintosh Application

• There is a Macintosh client called Fetch 5.3.for Macintosh.
• It can found http://ist.mit.edu/
• Select software : File transfer – Macintosh
• Direction for installing and using Fetch are located here:
• http://ist.mit.edu/services/software/fetch/53

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