This track shows the placements of the BCGSC Human BAC Re-Array, a curated "32k set" of bacterial artificial chromosome (BAC) clones that represents a minimal-overlap tiling path across the human genome. The clones are available for ordering from BACPAC Genomics at the Children's Hospital Oakland Research Institute (CHORI), where additional information on the collection, chromosome-specific sub-plates and quality control can also be found.
The set was assembled by the BC Cancer Genome Sciences Centre (Marco Marra lab) together with the BACPAC Genomics group at CHORI to provide a compact, redundant-free clone collection for physical mapping, functional genomics and array-based assays such as comparative genomic hybridization (CGH) and FISH.
The 32k set was selected from the human physical fingerprint map so that every region of the map is represented at least once. Additional clones were added to fill regions that initially lacked coverage, resulting in an average resolution of approximately 46 kb between overlapping BAC segments. The set provides coverage for more than 99% of both the fingerprint map and the reference genome assembly.
Most clones in the set (about 30,388) are drawn from the RPCI-11 and RPCI-13 human BAC libraries; a smaller contribution (about 2,062 clones) comes from the CalTech CIT-D library (CTD). Unlike the other tracks in this container, the 32k set does not rely on BAC end sequences: clone identity and assembly placement have been verified repeatedly by HindIII fingerprinting at the Genome Sciences Centre.
Each item represents the genomic placement of a single BAC clone in the 32k re-array, labeled with its clone name (e.g. RP11-…, CTD-…). Clicking a clone opens a detail page with a link to the corresponding BACPAC Genomics clone record, where ordering and additional clone metadata are available.
The original placements were generated by CHORI/BACPAC by lifting an earlier clone set onto GRCh38/hg38 from older assemblies. The pre-lifted BED file provided by BACPAC was downloaded from bacpacresources.org, the custom-track header lines were removed, the data were sorted and the file was converted to bigBed (BED5) format with bedToBigBed.
Note: earlier supporting data such as the original HindIII fingerprints and BAC end sequences for this minimal set are no longer available from BACPAC Genomics.
The data can be explored interactively with the Table Browser or the Data Integrator, and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our REST API, using track=bacRearray32k.
For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server as bacRearray32k.bb. Individual regions or the whole annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/cloneEnd/bacRearray32k.bb -chrom=chr21 -start=0 -end=100000000 stdout.
The original annotation source data can be downloaded from BACPAC Genomics. Additional information about the clone collection, including ordering, chromosome-specific sub-plates, and quality control, is available on the BACPAC Human BAC Minimal Tiling Set page.
The 32k Human BAC Re-Array was generated in collaboration between BACPAC Genomics at CHORI (Pieter J. de Jong and colleagues) and the BC Cancer Genome Sciences Centre (Marco Marra lab), Vancouver, BC, Canada. We thank Pieter J. de Jong for providing the pre-lifted hg38 placements. The RPCI-11 and RPCI-13 source libraries were constructed at the Roswell Park Cancer Institute.
Krzywinski M, Bosdet I, Smailus D, Chiu R, Mathewson C, Wye N, Barber S, Brown-John M, Chan S, Chand S et al. A set of BAC clones spanning the human genome. Nucleic Acids Res. 2004;32(12):3651-60. PMID: 15247347; PMC: PMC484185
Osoegawa K, Mammoser AG, Wu C, Frengen E, Zeng C, Catanese JJ, de Jong PJ. A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res. 2001 Mar;11(3):483-96. PMID: 11230172; PMC: PMC311044