| Library
Array Distribution Policy |
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Most arrayed libraries are available
in frozen "microtiter dish" format to academic and
non-academic users provided that there is a scientific need
for complete-library access. (for instance to annotate, modify
or analyze all BAC clones as part of a genome project). Commercial
users need to establish a licensing agreement. The clones
or derived DNA samples shall not be transferred
to other laboratories or used within commercial applications
without a licensing agreement. All users of whole libraries
will need to establish a signed Materials
Transfer Agreement (MTA). Materials Transfer Agreements
will need to be executed for commercial use with the owners
of the library clones used. For example, most libraries of
the type "RPCI-#" were prepared at Roswell Park
Cancer Institute, Buffalo, NY and are subject to the technology
transfer rules of RPCI. Libraries starting with "CHORI-"
were prepared at the Children's Hospital Oakland Research
Institute in the BACPAC Resrouces Center and are subject to
the technology transfer rules of CHORI. Please contact Pieter
de Jong (pdejong@chori.org) to inquire about this.
There is no warranty
of suitability of the DNA preparation for the user's application.
While we don't assume financial liabilities,
we recommend that users test the compatibility with their
proprietary protocols by ordering a subset of test clones
or DNA prep samples, prior to ordering the whole set.
When the scientific
results obtained from use of any library are published or
otherwise disseminated, the scientific creators and the origin
of the BAC library should be acknowledged. A recommended reference
will be posted on the respective library webpage as soon as
it is available. Please contact Pieter de Jong (pdejong@chori.org)
to post reference. This is important to permit us to measure
the impact of our scientific contributions and will facilitate
continued funding of similar resources.
Please note that
arrayed libraries are NEVER distributed immediately because
of the logistics of the library duplication and shipping.
The following considerations are important with respect to
the availability of library copies and the timing of the distribution:
1) Arrayed clone libraries
take up significant freezer space. Hence, we prefer
to maintain minimal inventories of clone collections
and often lack uncommitted copies of the requested library.
To appreciate the cost aspect: a typical mammalian genomic
BAC library with 10-fold genome redundancy (150 kb or
more insert size) has 550-700 microtiter dishes. A single
library copy takes up 20% of a large 21 CuFt freezer.
At the electricity rates in California, a single freezer
is approaching a $200/mo charge. Hence, each uncommitted
library copy costs about $40 electrical costs per month
to maintain in inventory.
2) Arrayed
library clones suffer from repeated freezing and thawing.
In order to replicate an arrayed library, the master
copy needs to be thawed and refrozen. To maintain viability
in the master copy, it is essential to pool requests
for library copies. Pooling of request affects the labor
costs to prepare copies.
3) Some libraries
are more popular than others. This depends on the species,
the number of scientists involved in genomic studies
for the particular species and other factors. We expect
that a hypothetical "elephant" BAC library
will not get as many users as a human BAC library. To
estimate the level of use and to identify possible users,
we invite scientists interested in copies for less popular
libraries to assist us to find interested colleagues.
This will facilitate scheduling of library replication.
Please realize that availability may require patience
for many months. In many cases this will be much quicker.
If we have no additional library request and a copy
will need to be prepared exclusively for the requester,
then the price will be adjusted to reflect the increased
labor costs.
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| Logistics and
technical aspects |
1) Libraries are in microtiter
dishes (mostly with 384-wells) and the wells contain
frozen clone cultures in LB media supplemented with
7.5% glycerol and an appropriate antibiotic (chloramphenicol
in BACs and fosmids; kanamycin in PACs; ampicillin in
cDNA clones).
2) The dishes
are covered with a regular lid only and the wells are
not sealed.
Hence, the shipment will need to occur in containers
with dry ice to prevent cross-contamination. All dishes
are packed together in blocks of 7 dishes (for 384 well
dishes) in Styrofoam boxes with dry ice.
3) Dry ice
will evaporate during the shipment. Hence we will use
sufficient dry ice to permit shipments to last at least
three days within the USA/Canada or 4-5 days for international
shipments.
4) The CO2-vapors from the dry-ice
will dissolve in the frozen culture media inside the
wells. This can have unexpected consequences. If the
plates are subjected to rapid temperature increase,
the carbon dioxide will form small gas bubbles inside
the frozen culture, resulting in an increased liquid
level - possibly rising above the rim of the well. Please
make sure that the dishes are immediately transferred
to -80 freezers for several days before thawing the
dishes - to permit the excess CO2 to evaporate slowly.
No dry ice should ever be stored in the same freezer. |
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