| FAQ - Screening Questions |
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How to Screen
- Who can use the ICCB-Longwood screening facility?
- Can I stay near the Longwood Medical Area if
I am an out-of-town screener?
- Is there a fee for using the ICCB-Longwood screening facility?
- What is the first step for screening at ICCB-Longwood?
- What does the screening facility staff do?
- How long does screening take?
- How far in advance should I schedule my screen?
- I cannot screen during normal hours (9 AM to
5 PM). Will I still be able to screen?
- Has someone already performed my type of assay?
Should I contact them?
- How do I gain access to the screening facility?
- I will not be able to make my screening appointment.
How far in advance should I contact you?
- What libraries should I start with?
Equipment/training
- What do I need to buy?
- What equipment is available for screening? How
do I receive formal training on the machines?
- What plates should I use?
Data Generation/Storage
- How do I store the data that my screen generates?
- What format should I use for my results?
Follow up/ Cherry Picking/Publication of Results
- I'm done screening a library, what's next?
- How do I request cherry picks?
- How should I acknowledge the ICCB-Longwood in publications?
- Should I specify in my publication the sources
of the commercial compounds that I screened?
How to Screen
1. Who can use the ICCB-Longwood screening facility?
The ICCB-Longwood screening facility is available only
to academic collaborators. Currently Harvard Medical School and Harvard Hospital-affiliated researchers are eligible to use the ICCB-Longwood Screening Facility. The facility shares many resources with the National Screening Laboratory for the Regional Centers of Excellence in Biodefense and Emerging Infectious Disease (NSRB; supported by a grant from the NIAID). Most investigators using the ICCB-Longwood/NSRB facilities
are in the process of developing or carrying out high throughput
screens of small molecule libraries. However, as the screening
schedule allows, we also host collaborators carrying out genome-wide
RNAi screens, and individual investigators, usually from the Harvard
Longwood Medical Area, who wish to use our plate readers or liquid
handling instruments to carry out small, non-screening projects.
2. Can I stay near the Longwood Medical Area if I am an out-of-town screener?
Temporary Housing for Visiting Screeners
List of short-term housing options from Harvard Medical School
(http://www.hms.harvard.edu/operations/vh/guesthouselist.html)
The following hotels and inns are within walking distance of the
screening facility:
The Beech Tree Inn
83 Longwood Avenue
Brookline , MA 02446
617-277-1620
http://www.thebeechtreeinn.com/
Inn at Longwood Medical
342 Longwood Avenue
Boston , MA 02115
617-731-4700
Longwood Inn
123 Longwood Avenue
Brookline , MA 02446
617-566-8615
http://longwoodinn.boston.swbd.net/
Marriott Courtyard in Coolidge Corner
40 Webster Street
Brookline , MA 02446
617-734-1393
For longer stays, it is sometimes possible to rent a room on a monthly
basis at Vanderbilt Hall, Harvard Medical School 's student dormitory
(http://www.hms.harvard.edu/operations/vh/vsapplication.html). The
application should be filed in the name of the person who will be
staying at Vanderbilt.
3. Is there a fee for using the ICCB-Longwood screening facility?
In the near future, fees for screening at ICCB-Longwood will likely be instituted. Currently, all users
are expected to provide their own screening supplies and reagents
(see "What do I need to buy?" below).
Collaborating groups are also expected to provide the personpower to carry out
assay development and screening. In exchange for access to our screening
expertise, compound collection, and automation, we require that all collaborators
submit their annotated screening data to our screening results database. More
information about data deposition is available in the ICCB-Longwood Data and Protocol
Sharing Agreement (see the
Data Sharing Agreement (PDF)).
4. What is the first step in screening at the ICCB-Longwood?
There is a screening application process to minimize
the waiting list and to prioritize new screening projects appropriately.
All investigators interested in screening at ICCB-Longwood, must submit an application via this website (see Screening
Application). Note that an application must be submitted each
time a new screen is proposed, even by investigators already collaborating
with the ICCB-Longwood.
5. What does the screening facility staff do?
Screening facility personnel schedule all screens, execute
all compound transfers, and train screeners in use of equipment.
They also maintain and repair the equipment and carry out technology
development projects. The screening facility staff do NOT read assays or
perform any steps other than compound transfer, some liquid handling, and
cherry picks. Please consider whether you will need assistance from someone
in your group for certain stages of your assay preparation
and reading, and plan ahead so that you are not shorthanded at a critical point.
6. How long does screening take?
The duration of a screen depends on many factors, including the
number of plates screened, how many steps the assay requires, and
the sample incubation times. In practice, screeners typically have
a throughput of approximately 20 plates in duplicate per day (40
plates total, or roughly 14,000 wells) for screens involving mammalian
cells. Throughput is somewhat higher for microbial screens. An
average ICCB-Longwood screening project assays a total of 50,000 to 100,000
compounds for biological activity.
Some data on plate processing times on various pieces of equipment
are given below to assist in making estimates. The facility staff
will also help you estimate the time you will need for your assay.
Plate dispensers take 10-30 seconds to fill a single 384-well
plate with a single reagent, depending on the volume that is dispensed.
Some dispensers are equipped with a stacker that can handle 25
plates, and the change-out time is perhaps 20 seconds per plate.
On average, the pin transfer robots complete one transfer every
1.5 minutes. Approximately 20 library plates can be transferred
to assay plates in duplicate in 60 minutes. However, some assay
protocols may require that compound transfer is staggered over
time.
Depending on the reading protocol and instrument used, plate
readers take 1.5 to 6 minutes to read a single 384-well plate;
this includes loading and reading the plates. Some readers are
equipped with stackers with a 50-plate capacity.
Imaging with the automated microscopes takes 45 to 90 minutes
per 384-well plate, depending on the number of sites imaged per
well, and the number of different wavelengths examined per site.
7. How far in advance should I reserve a slot for a screen?
The screening facility operates on a busy schedule
and is often fully booked two weeks in advance. Therefore, it is a good idea
to contact us several weeks before you want to start your screen. This is also
useful because it allows for training/practice with the instruments.
8. My schedule precludes me from screening during normal
hours ( 9 AM to 5 PM). Will I still be
able to screen?
In the screening facility we understand that
schedules are sometimes tight and we will do our best to accommodate
all screens. Reasonable arrangements can be made in advance.
9. Has someone already performed my type of assay? Should I
contact them?
At the screening facility, we have a database
of assays carried out at the ICCB-Longwood including associated, submitted
data. This is a wonderful resource for troubleshooting your assay
and expediting target identification. We will be glad to put you
in touch with other researchers. By talking to another screener,
you will be able to fine-tune your assay and evaluate your results
more rapidly.
10. How do I gain access to the screening facility?
After your application is accepted and you
have met with the Director, your Harvard ID card can be
activated for entry in the screening facility. The system card roster
is updated monthly and your card will be deactivated following completion
of your screen.
11. I will not be able to make my screening appointment. How
far in advance should I contact you?
The sooner you can inform the screening facility staff, the better.
If you must cancel a pin transfer request, PLEASE NOTIFY THE SCREENING ROOM IMMEDIATELY
at iccb_screen@hms.harvard.edu or 617-432-5815. It is vital to prevent stock plates from
being thawed unnecessarily, because repeated freeze-thaw cycles compromise the quality of
the libraries. Disregard for the cancellation policy or continuous
cancellations/tardiness may result in indefinite suspension of screening privileges.
12. What libraries should I start with?
Detailed descriptions of all our compound libraries
can be found on the Compound Libraries page. For information on the order in which we recommend that you screen the libraries in our collection, you can download the PDF "Recommended Screening Priority for Compound Libraries". All of the commercial libraries in our collection
are equally diverse. It is best to pilot your screen initially
with a 2000 - 3000 member library. Cell-based assays should
start by screening libraries of known bioactive compounds.
Equipment / Training
1. What do I need to buy?
The screening facility provides
access to the compound libraries and a variety of high-throughput
screening equipment. Screeners are responsible for all disposable supplies associated
with their assays. Some of the supplies you may need include:
- assay plates
- disposable pipette tips
- plate sealing supplies for assay plates
- reagents, buffers,
culture media
etc. A final list of supplies
that you must provide for your screen will be drawn up after consultation
with the screening staff.
Information about where to purchase screening
supplies can be obtained from the Screening
Supplies page For logistical purposes, screeners may choose to ship supplies
directly to the screening facility at the following address:
ATTN: Stewart Rudnicki
ICCB-Longwood
Harvard Medical School
Seeley Mudd 613, 250 Longwood Avenue
Boston , MA 02115 USA
tel.: 617-432-5815
2. What equipment is available for screening? How do I receive
formal training on the machines?
The equipment in the screening facility has
been purchased with a variety of assay possibilities in mind. Prior
to screening, you should contact the screening facility staff to
discuss the equipment you might use and to arrange the necessary
training. Descriptions of the screening facility equipment can be
found in the Screening Technology pages (Screening
Facility and Screening
by Imaging).
3. What plates should I use?
The pin transfer robot is most often used
for 384-well assay plates but it can also easily transfer compounds
to 96-well plates.
For maximum compatibility with our equipment, we recommend Nunc or Corning plates
(see Screening Supplies for more information).
Use of other plate types may be allowed if the plate is compatible with the equipment
.
Please contact screening facility personnel for questions regarding
plate formats.
Data Generation / Storage
1. How do I store the data that my screen generates?
An ICCB-Longwood server account
will be established in your name
so that
you can save and access data on our network. DO NOT
STORE YOUR SCREENING DATA ON THE HARD DRIVES OF THE COMPUTERS
IN THE SCREENING FACILITY. All data files are deleted from these
hard drives once a week. Please store all your data in your ICCB-Longwood
server account. You will be required to submit your data to the
ICCB-Longwood screening database before you can follow up on your primary
screen.
Most data files generated on the plate readers are small (*.txt
format) and
can easily be transferred back to your lab using portable memory devices (e.g.,
CDs, flash drives).
2. What format should I use for my results?
Before you start your screen, you will meet with David Wrobel
to discuss data formatting. Each plate reader's software has its
own specific filing system. It is possible to export your results
to text files
that
can be
easily read by most spreadsheet software available both for PC
or Mac.
Detailed instructions for data formatting and deposition may be viewed here (PDF).
Follow Up /Cherry Picking
1. I'm done screening a library. What's next?
You must submit your data to the ICCB-Longwood
screening database. After depositing and analyzing your primary
screen data, you will choose "positives" to follow-up in secondary
screens. For this purpose, we will provide you with 1μl
of each of your positive compounds, called a "cherry pick." You
will not be able to request cherry picks before your data has
been submitted for entry into the ICCB-Longwood screening results database.
You may request a maximum number of cherry picks equal to 0.3%
of the number of compounds you screened. For example, if you screened
a library of 16,320 compounds, you can request a maximum of 50 compounds
to be cherry picked. Exceptions to this rule can be made, if adequately
justified; please contact the Head of Screening.
Often screeners have a slightly higher than 0.3% hit rate and narrow
down their cherry pick choices by looking at the structures of their
hit compounds and by comparing their data with others' screening
data. This requires data entry into the screening database and also
time spent by the researcher mining the database. This step is usually
an important one in the success of the project.
2. How do I request cherry picks?
Cherry pick requests should be sent to David Wrobel and are generally filled within 7-10 days.
Instructions on how to request cherry picks can be viewed here.
Compounds will be plated in 384-well plates. If you need more
than 1 ul of compound, you can order it directly from the library
provider (see the Chemical
Libraries page) or discuss your request with the Screening Facility staff members.
3. How should I acknowledge the ICCB-Longwood in publications?
In the Acknowledgements section of their publications, we request that
investigators simply mention the ICCB-Longwood screening facility and, if
appropriate, specific staff members with whom they worked.
If an ICCB-Longwood member has made an
important intellectual contribution to the project, as determined
by generally accepted criteria for academic collaborations, then
that person should be considered for authorship on the publication.
4. Should I specify in my publication the sources of the commercial
compounds that I screened?
Yes. Compound library vendors appreciate public mention and
formal documentation of successful hit compounds from their collections.
Publishing this information helps the ICCB-Longwood negotiate favorable
pricing on future compound purchases.
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