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 Home > Resources > Libraries
   CHORI-17: Hydatidiform Mole (Homo sapiens) BAC Library   

Background information

The CHORI-17 Library was created from a transformed hydatidiform-mole cell line by Mikhail Nefedov in Pieter de Jong’s laboratory at BACPAC Resources, Children’s Hospital Oakland Research Institute. The haploid human BAC library was proposed in a white-paper proposal authored by Drs. Evan Eichler, Urvashi Surti & Roel Ophoff, dated October 10, 2002. This proposal can be downloaded in PDF format from the web site of the National Human Genome Research Institute. The preparation of the library followed the cloning approach developed in our laboratory (Osoegawa et al., 1998). DNA was isolated from cells of a well characterized haploid cell line (CHM1htert). This cell line was prepared at the Pittsburgh Cytogenetics Laboratory following Institutional Review Board approval for obtaining & handling of samples from human subjects. The cells were kindly provided by Professor Urvashi Surti, Director of the Pittsburgh Cytogenetics Laboratory. University of Pittsburgh School of Medicine. High-molecular-weight DNA was isolated following embedding of the cells in 0.5% agarose gel. The embedded DNA was partially digested with a combination of EcoRI restriction enzyme and EcoRI methylase and size fractionated by pulsed-field electrophoresis. DNA fragments from the appropriate size fraction were cloned into the pBACGK1 vector between the two EcoRI sites. The ligation products were transformed into DH10B (T1-resistant) electro-competent cells (Invitrogen). The library has been arrayed into 480 (384-well) microtiter dishes and has subsequently been gridded onto ten 22x22cm nylon high-density filters for probe hybridization screening. Each hybridization membrane represents over 18,000 distinct BAC clones (48 dishes), stamped in duplicate. Library characterization was performed by Teresa Ren and Jeff Garnes.

Users of the library are requested to acknowledge this in resulting publications: “The BAC clones from the hydatidiform mole were created at BACPAC Resources by Drs. Mikhail Nefedov & Pieter J. de Jong using a cell line created by Dr. Urvashi Surti". Large scale use of the library for any application should be considered a collaboration, which should involve appropriate scientific credits. Please contact Pieter de Jong prior to publication.

BAC library construction was funded by NIH grant HG025323-03 under the auspices of the NIH-funded BAC Resource Network.

Segment

1

2

All

Vector

pBACGK1.1

pBACGK1.1

pBACGK1.1

Restriction Enzyme

EcoRI/EcoRI Methylase

EcoRI/EcoRI Methylase

EcoRI/EcoRI Methylase

DNA Source

N/A

N/A

N/A

Plate Numbers

1-240

241-480

1-480

Plate Count

240

240

480

Empty Wells

3345 (3.63%)

3918 (4.25%)

7557 (4.1%)

Non-Recombinant Clones

N/A

N/A

N/A

Non-Insert Clones

Approx. 3215 (8/221, 3.62%)

Approx. 406 (1/217, 0.46%)

Approx. 3778 (9/438, 2.05%)

Recombinant Clones

85600

87836

172985

Average Insert Size

199 Kbp

194 Kbp

197 Kbp

Genomic Coverage

5.7X

5.7X

11.3X



Click here for a legend of the previous tables.

Data on the CHORI-17 clone insert size distribution has been determined by pulsed-field gel Electrophoresis. Clone Size Distribution has been plotted graphically.

The library is available for individual clone orders distributed as agar-stab cultures. Clones can be identified through screening of "high-density colony" hybridization filters . Please visit the ordering information page if you want to place an order.


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 questions about hybridization membranes, please contact BACPAC Resources (BACPACorders@chori.org).

Resources:
Many CHORI-17 BAC clones have been insert-end sequenced and fingerprinted (HindIII-restriction-fragments). The BAC-end-sequences (BES) corresponding to the end-sequenced BACs can be retrieved from the NCBI Trace Archive. with the query string [library_id="CH17"]. To find the BAC-end-sequences for any specific clone (if it has been sequenced!) use the query string [clone_id="CH17-224P20"] to retrieve, for example, the sequences for clone CH17-224P20.

How can one find the CHORI-17 BAC clones displayed within the UCSC Browser? Please, first upload (by Copy & Paste) the following links to the UCSC Browser Custom Track Upload: "http://bacpac.chori.org/download/ch17_hg18/ch17.bed" for the hg18 human genome assembly or "http://bacpac.chori.org/download/ch17_hg19/ch17.bed" for the hg19 human genome assembly. After uploading, the CHORI-17 BACs will only be visible for a couple of hours. They can be found displayed after searching for any specific gene or genomic region. See, for example, the following map (PDF) for CH17 BAC clones representing the FUS gene. Another map depicts an arbitrary 1 Mbp region of chromosome 21.

Posted: December 6, 2004. Revised: December 7, 2004. May 4, 2010.

 

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