Site Search by Google

Products

Libraries
Clones
Mapped Clones Collection
Human "32k" BAC Re-Array
Filters
Vectors

Filter Analyzer new

Services

Library Screening Svc.
DNA Isolation Service
Library ReArraying Service

 

 
  
 Library Screening Services    

BACPAC Resources has established a library screening service to assist end-users with identifying BAC clones from our collection of >100 genomic libraries. Primary screens are performed via hybridization using synthetic oligonucleotide probes (an Overgo). The overgo probe is generated by ordering 24-mers containing an 8 base pair overlap. The probe is made radioactive in a fill-in reaction containing 32P-dATP, 32P-dCTP (Mc Pherson et al.). The resulting probe is a highly specific 40mer after denaturation and inclusion in a hybridization reaction to 22x22cm nylon filters containing BAC clones spotted in duplicate. Each nylon filter contains the contents of 48 microtiter dishes X 384 wells/dish totaling 18,432 clones spotted in duplicate.

Quotes provide end-users with an estimate for cost associated with a screening project; all quotes are valid for 30 days. BACPAC Resources assumes the financial liability for unsuccessful screening projects consequently end-users are billed on a cost recovery basis. End-users only pay for successful probes that identify probe-positive BACs verified in the secondary PCR confirmation assay.

Library screening service*
Option I: per gene Price
BAC-library screening basic charge including two bracketing probes for one genomic location. $2,500.00
For each additional genomic location including two bracketing probes for one genomic location. Additional probe pairs can be added to one hybridization. $300.00
Above service includes at least one positive BAC per gene confirmed by PCR.**
Option II: per region*** Price
Large-region screening with one probe at every 50 kb for 1 mega-base genomic region. $5,500.00
For additional mega-base region with one probe at every 50 kb. $1,200.00
Above service includes a set of BACs with positive signals where PCR on pooled BACs confirms the region at every 150 kb. If you require identified BACs by PCR or BAC-end sequencing, refer the below table.

BAC clone charge and optional service
BAC clone charge Price
Single BAC clone - verified by PCR. $100.00
Indexed single BAC clone - where both ends have been sequenced for mapping purposes (BAC-end sequencing). $300.00
Optional service Price
miniprep BAC DNA (>1 ug of crude DNA, suitable for PCR, E.coli transformation and restriction digestion analyses) $60.00
midiprep BAC DNA (>50 ug of high-quality DNA, suitable for transfection) $140.00
Size check of BACs determined by NotI (insert size) and PI-SceI (linearization) restriction digestion followed by gel electrophoresis (flat price up to 10 BAC clones). $200.00

Additional charge
Handling fee Price
Charge for each package $35.00
Shipping charge Price
Domestic (additional charge applied for larger packages) $35.00
International (additional charge applied for larger packages) $55.00+
The genomic resources will be shipped by Federal Express or DHL/Airborne Express on either recipient's or BACPAC's account.

Prices are subject to change without prior notification

Filters are available only as complete library sets or segments at $200 per membrane (http://bacpac.chori.org/filtersAvail.php).

* The price is estimated according to typical mammalian libraries with 240-480 plates of 384-well microtiter dishes. Libraries outside of the typical rang of plates will be quoted individually.

** All positive clones by hybridization and gene-specific PCR will be included. A limited number of BAC libraries (such as CHORI-216, CHORI-219, CHORI-303 constructed from the genomes of Xenopus tropicalis, Xenopus laevis, and Sea Lamprey respectively and others) are subject to a non-refundable set-up fee of 50% of the quoted price, if the screening does not provide any positive signals for those libraries.

*** Large-scale screening of above 5 Mb will be quoted individually.

 Target  Information / Probe Design / Secondary Screening

End-users provide the following: (1) the library name requested for screening, (2) an accession number for the target sequence, (3) and information describing the region within the target sequence for the probe design e.g.

Library: RPCI22 Mouse BAC Library

Target description: myosin, heavy polypeptide 6, cardiac muscle, alpha (Myh6)

Accession: NM_010856

Description: target a region 5kb upstream of Exon 4, and 5kb downstream of Exon 5


DNA sequence within the target region is analyzed using a probe design script; optimal probes sequences are checked for target specificity using bioinformatics tools on The UCSC Genome website (http://genome.ucsc.edu). Overgos that hybridize to the target sequence, are in conserved regions of the genome, and don't contain repeat sequences are optimal probes.

Probe-positive clones are verified via PCR therefore oligos required for the secondary screening are ordered in conjunction with oligos for the overgo probe. PCR primer design is included in the cost for the screening consequently primers sequences are not required from the end-user. However if an end-users has PCR primers previous verified to generate a single band when tested using total genomic DNA and the primers are within 5-10kb of the target sequence please include the sequences.

  Quote Processing

End-users receive a quote containing relevant information on the library requested for screening, the gene target and cost for the screening; a Payment Request Form is also included with the quote. Once the quote has been accepted and the Payment Request Form returned the project begins. Required information for inclusion into the quote:

Name:

Institution:

Mailing address:

Phone #:

Fax #:

Email address:

 Frequently Asked Questions

What does 10X genome equivalents mean (haploid genome)?

Genome redundancy is calculated as follows: Clones insert size (kb) x number of clones / size of the genome (kb); the depth of the library. A 10X redundant library contains 99% of the DNA sequences in the genome. On average 10 BAC clones are expected to contain the target DNA sequence in a 10X library; 5 clones per haplotype.

How long does the library screening take after submission of the completed documents?

The library screening process takes 4-6 weeks on average for completion. Laboratory closure during Institutional Holidays can affect the timelines for project completion.

  Technology Development

Modified cloning vectors for making gene knockout constructs and vectors that facilitate BAC-end sequencing are actively being pursed in our laboratory. The BACPAC Resource Center has and will continue to explore methodologies utilizing BACs for downstream applications.

 

  Disclaimers


BACPAC Resource Center is a non-profit organization dedicated to generating and making recombinant clone library resources available to the scientific community. Screening high-density colony filters is an experimental endeavor added to the list of services intended to aid researcher with the identification of BAC clones for downstream analysis.

Methodologies used to screen recombinant clone libraries are robust and well documented. However some DNA sequences can be problematic posing difficulties for overgo probe design and colony hybridization. The BACPAC Resource Center will make a good faith effort to start and complete all services on time and will notify end-users if unforeseen problems are likely to cause substantial delays.

The BACPAC Resource Center does not guarantee that the received clones are compatible with all down-stream applications.

The BACPAC Resource Center does not guarantee that the clones in each well are a homogeneous population. We know that a limited amount of well-to-well cross-contamination occurs and is unavoidable when handling arrayed libraries.

The BACPAC Resource Center reserves the right to discontinue service for probes and/or problematic DNA sequences. If it is deemed necessary to discontinue the library screening there will be no charge to the end-user.

Neither BACPAC Resource Center nor the end-users shall be responsible for failure or delay in performance of its obligations related to the services due to causes beyond its reasonable control, included but not limited to governmental actions, fire, labor difficulty, shortages, civil disturbances, transportation problems, interruptions of power or communications, failure of suppliers, or natural disasters.

  Contact

For more information, please send inquiries to libraryScreening@chori.org

 

For questions related to the site, please contact webmaster.
The use of this website is subject to the terms of use.