Names and other identifying information have been removed
from any correspondance listed on this page.
clone you have ordered does not appear to be the correct clone.
2. How can I read the results
from the hybridization of the filters I ordered?
3. How do I handle the clones that
I just received
4. I am interested to work with genes
of the Pseudoautosomal region of cattle and I would be grateful
to you if you could send me the BAC clones for the genes in
the PAR region of Cattle.
5. I would like to order a BAC clone I have
seen in a publication. The name is RP11-469H8. I don't see
this clone listed on your web site. Can you let me know you
have it and how I can order it?
I have a human BAC clone RP11-96I16
of chr 18 for the n-cadherin gene and am trying to find the
sequence information of this clone. I went to the ucsc site
but it does not list the BAC clone. Where can I get the sequence
in fasta format for this clone?
recently ordered several clones from your recource center.
Now I am wondering if the clones have already been sequenced,
which would save us a lot of time and money. The clones are
481B2, 535B14 and 552N21. Can you indicate where I can find
the sequence information? [phone
message, August 31, 2005]
ordered five clones from the RP11 human BAC library. Four
of the clones contain the sequences I am interested in, but
number "5" was wrong! Can you, please, correct
this as soon as possible? We urgently need the clone and have
lost much time working with the wrong clone. Is there any
warranty with respect to the clones? [frequent
and unfortunate misunderstanding]
obtained two BAC clone named "RP23-104D19 and RP23-190J3
and I would like to know the name of vector of these clones.
Which BAC vector did you use to generate these clones? [frequent
type of question]
I would like to order a mouse BAC clone containing the entire
CDK2 locus. How can I find the ID number (name) of the corresponding
would like to find a BAC clone containing a human gene named
would like to order a mouse BAC with the name MSMg01-88E21.
The BACPAC shopping cart does not recognize this clone. Why?
have seen BAC clones from the NOD mouse strain in ENSEMBL.
Does BACPAC distributes these? The BACPAC shopping cart does
not recognize " bCN538a05".
14) I would like to find a BAC containing the Drosophila melanogaster gene "GAF". How can I identify such a clone? The BACPAC website does not appear to have this information.
15) Can the map-confirmed human BAC clone set of ~32,000 BACs ("32k-set") be displayed in the UCSC Human Genome Browser? We would prefer ordering clones with minimal risk of being mismatched with mapping data.
A clone you have ordered does not appear to be the correct
2 BACs from you from the RPCI23 mouse BAC library; clone numbers
RP23-201B12 and RP23-301F3. These 2 clones are supposed to
contain genomic fragments of a mouse gene which is located
on chromosome 1. However, I was unable to PCR-amplify any
sequence using the gene-specific primers. And when I subcloned
sequences from the RP23-265D16 clone, I got genomic sequences
belonging to mouse chromosome 10.
Where is the mistake
coming from? and what should I do? Maybe I ordered the wrong
clone, so here is the genbank document corresponding to one
of the clone (RP23-301F3) I wanted"
We have looked at
your request and tried to find a suggestion for the mismatch
between the clone ordered and the sequence it contained. We
looked at the history of the various replicates of the arrayed
BAC library. In the original 384-well dish (#301) obtained
after picking colonies, our records indicate well F3 had clear
medium, meaning no growth of bacteria. After replicating the
library for the first time, there was also no visual growth.
Only after a second replication cycle, the sterility of the
well was gone and the well was turbid, probably due to cross-contamination
from cells derived from one of the neighboring wells. I am
sure that your are aware that handling of thousands of microtiter
dishes can not be done under conditions of absolute sterility.
The remaining question is what the true identity of the clone
in the database is. I presume that the clone in the database
came from a copy of the library were well "F3" was
contaminated and possibly heterogeneous. There is no way for
us to know the true identity of the clone in the "master"
copy of the library - without contacting the laboratory which
originally screened the library and/or sequenced the clone,
and probably not without additional library screening. The
clone exists in our master-copy of the library, but likely
at a different address (well position) in the library. In
this particular case, we know from our record that the clone
must have come from a different well because our original
master copy had no growing cells as registered soon after
library generation. Hence, the well might have become populated
(in a replicate of the librray array) through well-to-well
contamination. In addition, clones can make "virtual
moves" within the arrayed library as a consequence of
typographical errors when the database record were established
or when the original clone name was incorrectly copied anywhere
along the process of handling the clone prior to sequencing.
We just do our best
to deliver what is most likely identical to your requested
clone and at the lowest possible cost - in most cases the
requested clones agree with the expectation (far over 90%
of the time).
How can I read the results from the hybridization of the filters
on how to read hybridization signals from our filters are
available in Microsoft Word format from our download
You can now also
use the Filter Interpreter Application
to interpret your filter hybridization results.
How do I handle the clones that I just received?
Please refer to
the clone handling page
I am interested to work with genes of the Pseudoautosomal
region of cattle and I would be grateful to you if you could
send me the BAC clones for the genes in the PAR region of
We cannot do this
for you, but we can provide you the clone if you give us the
coordinate in the library (for instance RP11-15G11 or CH201-14H1).
Here's a page with popular mapping resources that you can
use to obtain the clones of your interest: http://bacpac.chori.org/mapping_res.htm
since cattle genomes are not at advanced sequencing stages,
you will probably have to rely on gene expression data, which
may not be too helpful in deciphering genome mapping data;
In this case, try to go to Vancouver genome sciences center
where they have a java program called ice (internet contig
explorer) which allows you to browse fingerprinting data of
genomes in sequencing pipelines. They have a bovine database
in that program which may help you in finding the clone you
want provided that you have the appropriate markers for your
gene of interest. In last resort, if you cannot find the clone
for your gene of interest in the databases, you may want to
order from us a filter set for the genome of your choice and
do screening of these filters using an appropriate probe for
your gene, in this case you will end up with about 10 clones
(if the library is 10X redundant) that you can order from
I would like to order a BAC clone I have seen in a publication.
The name is RP11-469H8. I don't see this clone listed on your
web site. Can you let me know if you have it and how I can
Answer: We have
nearly 20 million distinct clones in our freezers at BACPAC
Resources, CHORI, Oakland. All these clones can be ordered
by following our ordering instructions http://bacpac.chori.org/ordering_information.htm.
We are not generating or maintaining data on most clones and
therefore, we do not separately list each clone. An exception
is a very small subset of clones isolated and characterized
from the original libraries. If the clone is part of this
small subset of mapped or otherwise characterized clones,
then you can find this on specific web pages on our site (see:
All other clones are maintained as part of microtiter dish-arrayed
libraries. Most likely therefore, you will not find the clone
as part of a characterized subset. This does NOT mean that
we cannot provide the clone. To find out if we have the requested
clone, you can follow any of two procedures described below:
First, you can dissect
the name of the clone into it's components. For instance RP11-469H8
indicates that the clone is part of the RPCI-11 BAC library
(abbreviated as RP11, see the NCBI
nomenclature rules: ). It is in 384-well microtiter dish
#469, Row "H" and column "8". You can
check the properties of this library by inspecting our library
You will find there a specific hot link to the RPCI-11 BAC
library page: http://bacpac.chori.org/hmale11.htm.
This library was prepared in our laboratory and is maintained
in 1,440 microtiter dishes numbered from 1 through 1440. The
dish #469 is a valid number in this range and is part of library
segment "2" prepared by cloning genomic DNA partially
digested with EcoRI into BAC vector pBACe3.6. Hence, we most
likely have this clone although we cannot guarantee that the
date in the publication or in public databases indicates the
correct clone. There are a significant number of incorrect
entries in databases due to data and sample tracking problems.
Hence if you order this clone from us, you will obtain viable
bacterial cells in a bacterial stab culture to be confirmed
in your laboratory and lacking a guaranteed identity. The
odds of an erroneous clone/data association is about 10-20%,
so please be aware and, please, check by PCR or another technique.
A second alternative
is to use the NCBI Clone Registry (for BACs & PACs, not
for cDNA clones): http://www.ncbi.nlm.nih.gov/genome/clone/index.html.
Enter the clone name in the registry and you will obtain an
answer if the clone has associated data in the NCBI database.
If the person publishing the clone has not entered the clone
into the database, you will obviously be out of luck. Following
hot links on the positive NCBI reply, you will arrive at a
page which summarizes all linked information. This page also
includes distributor information. In this particular example,
you will return to our contact information.
I have a human BAC RP11-96I16
of chr 18 for the n-cadherin gene and am trying to find the
sequence of this clone. I went to the ucsc site but it does
not list the BAC clone. Where can I get the sequence in fasta
format for this clone?
You are making the
same assumption many people make. It is wrong to assume that
all clones found in mapping databases and map browsers have
been sequenced. Most clones have NOT been sequenced.
Here is why:
All BAC libraries are generated by random cloning of large
DNA fragments. Any random process has a finite chance that
some genomic fragments are not present. The odds of
not having a complete genome representation increases with
small libraries. Therefore, most libraries are at least 10-fold
redundant and the human RPCI-11 BAC
library is more than 30 fold redundant. This resulted
in a minimal number of gaps in the genome represented in the
library. It also allowed the selection of a set of mapped
clones with somewhat minimal overlaps. The minimal overlaps
are important for the economy of the human genome sequencing:
shotgun sequence libraries were prepared from a minimal set
of BAC clones. Hence, while the RPCI-11 BAC library is >30-fold
redundant, less than 1.5-fold redundancy of the BAC
clones have been subjected to shotgun-sequencing. About 10-fold
redundancy of BACs have been mapped either by fingerprinting
or virtually mapped by BAC-end sequencing.
How does one find out if the clone has been sequenced?
There is no answer which is suitable for all the sequencing
projects and species. However, for the human genome and several
additional genomes, you should first go to the NCBI Clone
Registry. Type the name of the clone and find out all
mapping and sequencing information linked to the clone. If
you don't find any information, then there are two options:
you had a typing error in the clone name or there simply is
no information available for the clone. To avoid typing errors,
make certain that the name of the clone agrees with the NCBI
Please, realize that many sequencing centers are not maintaining
the clone names according to the nomenclature rules and you
may have to convert the clone name into the NCBI-recommended
name. In the example for the RP11-96I16 clone, you will find
the following registry information (follow this link).
If the clone registry indicates an accession number for a
high-quality or draft assembly of the BAC sequence, then you
have your answer. However, for most clones the only information
displayed indicates that the BAC-insert ends have been sequenced.
This is enough for map browser programs to map the BAC with
If the clone has NOT been sequenced, then you can
nevertheless retrieve the equivalent sequence from the human
genome. The "equivalent" sequence is derived
from the genomic coordinates corresponding with the cloned
fragment. This sequences is, however, derived from a different
haplotype and from a different set of clones & libraries.
Here is how you can retrieve the sequence. Go to the UCSC
Human Genome Browser (http://genome.ucsc.edu/cgi-bin/hgGateway)
and search for the clone name (in the correct NCBI nomenclature)
by pasting the name into the "Position" window,
replacing whatever text was already there. In the example
for the RP11-96I16 BAC, you will find that a map is displayed
bp (the approximate size of this BAC with the data based on
the May 2004 Assembly). This BAC has not been sequenced but
nevertheless the equivalent size is known with single base
pair resolution. This is not the real size of the BAC but
the size of the corresponding sequence from another haplotype.
Hence, it is likely that the sequence is different with on
average one SNP mutation per 800 bp and perhaps also insertion
or deletion events. You can do many things with the displayed
map. You can configure the map to display the BAC better (i.e.
activate the BAC-End Pairs option to "Full" and
then use the "Refresh" option on the web page -
not the internet browser). You can also retrieve the equivalent
DNA sequence, by activating the "DNA" button at
the top of the map browser. Success!
Can you indicate where I can find the sequence information
for clones I recently ordered? [phone message,
August 31, 2005]
Unfortunately, we are not a company but a not-for-profit
resource center attached to an academic laboratory. We have
created most of the BAC libraries in our repository and distribute
these clones to the scientific community. We usually don't
know why people order a particular clone and if there is any
information available about this clone. Most data has been
generated by other users of our libraries and deposited in
public databases. We do not have the personnel and time to
do data-mining services in public databases. The clone is
derived from a particular library and we post relevant information
on a libary-specific web page. This information can be found
in our library browser
As a courtesy, we sometimes find a few minutes in
between other work to help users of BACs find information.
Hence, I have spent a few minutes to find the complete clone
IDs for the clones your recently ordered from us. I use Google
Desktop to search all orders for recent orders with the partial
clone names you provided. The clones names were not unique
because you did not mention the library name or the species
name. Anyhow: Google desktop is a great invention!
I found your order
for clone RP22-481B2, RP22-535B14, etc. I am not sure how
you obtained the names of these clones. The name "RP22"
indicates the name of the BAC library (see our list of libraries),
which is derived from the 129S6/SvEvTac strain, which is
isogenic with some of the popular mouse ES cell lines. This
is usually why people are interested in "129"
BACs: to create targeting constructs from isogenic DNA.
is not one of the BAC libraries used for the mouse genome
project, Very few clones from this 200,000 clone library
have, therefore, been characterized or sequenced. We are
not the 'gate keepers' for the data generated from
our BAC clones. The best way to find out if there is any
data related to a particular clones is to search the NCBI
Clone Registry. The registry is not complete, but is
the best first approach. If the clone is not listed in the
clone registry, then try searching in Genbank with a text
search for the correct clone name. The correct clone name
should follow the recommended NCBI
clone nomenclature. The chance that you will find
information related to these clones is, however, very, very
small. As I mentioned, I have no idea how you found
these clone names. Perhaps you found these in the literature
and perhaps these were sequenced or mapped by somebody else?
Please let me know if this information was useful. Thanks.
We received one wrong clone. Please send us the
correct clone as part of your warranty service.
You order a clone
and once the clone arrives, it appears that it does not
contain the sequence attributed by the public databases
to this clone. The first reaction is a logical one: "you
paid for it and should get what you expect". Here is
why this is not the case. We cannot provide a warranty that
the databases are always correct. In fact, an error rate
of around 10% should be expected: good data associated with
the wrong clone name. As you will certainly understand,
we cannot become an insurance company providing warranty
services related to experimental data generated elsewhere.
Most of the clones
were generated in our laboratory. This process involves
streaking freshly transformed cells (prior to cell duplication)
on large square dishes with LB agar and the required antibiotics.
Colonies formed after an overnight incubation and these
were arrayed into separate wells of 384 well dishes by a
colony picking robot. All dishes (also known as "plates")
are labeled starting with plate #1 and going in a continuous
plate numbering to the final plate number in the library
(any number below 3,000). This is the stage when clones
also get there ad-hoc names. The naming convention is based
on the NCBI
clone nomenclature recommendations. This means, for
instance, that a clone from the RP11 library residing in
plate 128 at the intersection of row "D" and column
"15" will be labeled: "RP11-128D15".
When you order
a clone from us, we do not check public databases to find
out which sequences have been reported for a particular
clone, and do not determine if the sequences in the clone
are consistent with the database. It is not economically
feasible for us to check if the databases indicated the
correct clone. We will simply find the requested clone in
the freezer, then streak it to single colonies on a petri
dish with LB agar and the appropriate antibiotic. We then
take a single colony to inoculate an agar-stab culture (standard
microbiology) with the appropriate antibiotic. Hence, the
only thing we know about the clone being mailed, is that
it very likely was correctly retrieved and that it is still
viable (a fresh colony was obtained).
In nearly all
cases when a clone fails to meet the expectation (in about
10% of the clone deliveries), the database was incorrect.
In summary, we provide no warranty service.
However, we will - at your insistence and as a courtesy
- retrieve the same clone once more and ship it to you free
of clone retrieval charges (except that we ask you to pay
for the mailing costs). If you would like to receive a alternative
clone for the same gene(s), then a new order
will have to be placed online.
How do I find the name of the vector used for a
particular BAC clone?
Each BAC clone
is part of a BAC library. We have a specific web page for
each library which describes the common properties of all
clones for a particular library. How to know the library
name? The library name is embedded in the clone name according
to the NCBI
Clone Nomenclature recommendations.
In this case, "RP23" is the NCBI library name
and the full name of the library is "RPCI-23".
The NCBI also has a library
browser with all "approved" library names.
Our own web site also contains a library
browser with extensive detailed information on all BAC
libraries we distribute clones for. The default version
of this browser organizes the libraries according to a phylogenetic
tree of species. Alternatively, the libraries can be viewed
ordered by name as derived
from the abbreviated name of the originating institute.
Most of these libraries have been prepared in our
own laboratory (CHORI or RPCI). The specific page for the
RP23 mouse BAC library contains
the name of the vector: pBACe3.6 and a link
to the sequence and vector graphics.