| CHORI-216
Xenopus tropicalis BAC library |
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The CHORI-216 Xenopus tropicalis BAC library (segment 1)
has been constructed by Michael Nefedov in Pieter de Jong’s
laboratory at BACPAC Resources, Children’s Hospital
Oakland Research Institute. The preparation of the library
followed the cloning approach developed in our laboratory
(Osoegawa
et al., 1998). Agarose embedded DNA was obtained from
Chris Amemiya at the Virginia Mason Research Center as part
of a collaborative effort to create the Xenopus tropicalis
BAC library. The DNA was isolated at VMRI from a Nigerian
male frog in the 7th generation of inbreeding (N7). The frog
was part of the “Stock 248 F7A2” population maintained
by Robert M. Grainger, University of Virginia. Gender was
determined by visual analysis. DNA was isolated by embedding
erythrocytes in agarose. Agarose embedded DNA was partially
digested with a combination of EcoRI restriction enzyme and
EcoRI Methylase and the fragments were size-fractionated by
pulsed field electrophoresis. DNA fragments from the appropriate
size fraction were cloned into the pTARBAC2.1 vector between
the EcoRI sites. The ligation products were then transformed
into DH10B (T1 resistant) electro-competent cells (Invitrogen).
The library has been arrayed into 384-well microtiter dishes
and also gridded onto four 22x22cm nylon
high-density filters for screening by probe hybridization.
Each hybridization membrane represents over 18,000 distinct
Xenopus BAC clones, stamped in duplicate. Library characterization
will be performed by Qing Cao and Kazutoyo Osoegawa. An extension
of the library using a different restriction enzyme for generating
genomic fragments, is currently (January 2003) in progress.
This 2nd segment of the library will use MboI for partial
digestion. This work was funded by NIH grants HG01165-07SI
and HG025323-01 (Pieter J. de Jong, CHORI) and HG02526-01
(Chris T. Amemiya, VMRC).
Please note: The following data is provisional pending further
characterization.
| Segment |
Cloning Vector |
DNA Source |
Restriction enzyme |
Plate Numbers |
Total Plates |
Empty Wells |
Empty Wells (%) |
| 1 |
pTARBAC2.1 |
Blood |
EcoRI |
1-171 |
171 |
1,952 |
3 |
| Segment |
Non-insert clones (%) |
Non-insert clones (deleted vector) |
Non-Recombinant Clones (vector) |
Recombinant clones |
Insert Size (Average) |
Redundancy (Genome Size: 1700 Mb) |
| 1 |
0 |
0 |
0 |
? |
175 Kbp |
6.6 |
Click here for a legend of
the previous tables. Provisional data on the CHORI-216 clone
average insert size has been determined by Pulsed Field Gel
Electrophoresis. Clone size distribution will be posted on
this page as soon as available.
The library is available for academic users by reimbursement
of duplication costs (labor & materials), resulting in
a price of $20 per 384-well dish. Dishes can only be obtained
per complete segment ($3,420 for segment 1). We normally do
not maintain an inventory of extra library copies and requests
for library copies will usually meet delays of many months
up to one year. Several requests are pooled before initiating
library replication. Pleas review our policy. Shipping will
be done by Federal Express and charged to recipient's account
number.
Organized general distribution of clones and screening reagents
remains the exclusive activity of BACPAC Resources, unless
this service has ceased to exist. All library copies and individual
clones should be maintained using the recommended nomenclature
guidelines as posted by NCBI.
When the scientific results obtained from use of the CHORI-216
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 this page as soon
as it is available. Otherwise, please contact Pieter
de Jong (pdejong@chori.org). This is important to permit
us to measure the impact of our scientific contributions and
will facilitate continued funding of similar resources.
Please visit the ordering
information page if you want to place an order.
Academic and commercial users interested in a copy of the
BAC library should contact Pieter
J. de Jong (pdejong@chori.org, fax: (510) 450-7924). For
hybridization membranes, please contact BACPAC Resources (BACPACorders@chori.org).
Please contact Pieter J. de Jong or Kazutoyo Osoegawa for
questions related to this library.
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