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WIBR-1: Mouse Fosmid Library |
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The mouse Fosmid library was produced at the Whitehead Institute/MIT Center for Genome Research as part of the MGSC mouse genome sequencing effort. DNA from a female C57BL/6J mouse was sheared and genomic fragments of approximately 40 kbp were size-purified. The molecular cloning procedures made use of the "EpiFOS" fosmid cloning kit from Epicentre Technologies. The fragments were ligated to the blunt-ended fosmid vector and then mixed with bacteriophage lambda packaging extract. The resulting particles were used to transfect E.coli strain "EPI100" and library clones were picked into 384-well dishes.
The library has been used to assist in the assembly of the mouse genomic sequence using the paired-fosmid end sequences to link contigs from smaller insert clones.
The fosmids can found through various databases.
The mouse fosmid clones can also be viewed within the UCSC Mouse Genome Browser . Please find your favorite gene or genomic region following the instructions on the UCSC website. Then find the "Add Custom Tracks" button immediately below the UCSC genome map window. Click on this. This will open a custom upload page. Copy one of the URLs for the custom tracks from the bottom of our page and paste this into the UCSC upload window, then "Submit". Then search for the genomic region or gene of interest, and inspect the Browser display. The fosmids are initially displayed as a single "Dense" line on top of the display, but can be configured to display a tiling path of clones by selecting the "Full" display option. The URLs represent either the complete mouse fosmid library or chromosome-specific tracks (bottom of this page).
Mouse fosmids can be displayed within the ENSEMBL mouse browser but are not part of the default map display. To display the clones for a specific region, first load this region following ENSEMBL instructions. Then, configure the display using the "Configure this Page" button on the left. Look for the "External Data" option and click on this to open the set of choices. Select "DAS Fosmid end pairs" option and then "Save & Close" the Configure Page". The fosmid clones should now be displayed as horizontal bars and specific information can be found by clicking on any specific fosmid. The external clone names starting with "G135P...." can be used to order the clones from BACPAC Resources.
Finally, fosmid clones for specific regions may be found using the NCBI CloneFinder tool as explained in the BACPAC Question & Answer section (answer to question #10).
Unfortunately, the various databases use inconsistent names for the fosmid clones. BACPAC resources has made available a tool that allows for conversion of clone names between nomenclature formats. Please use the following link: https://bacpacresources.org/fosmidConversion.php to convert clones between different formats.
Segment | All | Entire Library | Vector | pEpiFOS5 |
| Restriction Enzyme | Eco72 I | N/A | DNA Source | N/A | N/A | Plate Numbers | 1-2893 | 1-2893 | Plate Count | 2893 | 2893 | Empty Wells | N/A | N/A | Non-Recombinant Clones | N/A | N/A | Non-Insert Clones | N/A | N/A | Recombinant Clones | 1110912 | 1110912 | Average Insert Size | N/A | N/A | Genomic Coverage | N/A | N/A |
https://bacpacresources.org/download/wi1_mm9/WI1.bed
https://bacpacresources.org/download/wi1_mm9/chr1.bed
https://bacpacresources.org/download/wi1_mm9/chr2.bed
https://bacpacresources.org/download/wi1_mm9/chr3.bed
https://bacpacresources.org/download/wi1_mm9/chr4.bed
https://bacpacresources.org/download/wi1_mm9/chr5.bed
https://bacpacresources.org/download/wi1_mm9/chr6.bed
https://bacpacresources.org/download/wi1_mm9/chr7.bed
https://bacpacresources.org/download/wi1_mm9/chr8.bed
https://bacpacresources.org/download/wi1_mm9/chr9.bed
https://bacpacresources.org/download/wi1_mm9/chr10.bed
https://bacpacresources.org/download/wi1_mm9/chr11.bed
https://bacpacresources.org/download/wi1_mm9/chr12.bed
https://bacpacresources.org/download/wi1_mm9/chr13.bed
https://bacpacresources.org/download/wi1_mm9/chr14.bed
https://bacpacresources.org/download/wi1_mm9/chr15.bed
https://bacpacresources.org/download/wi1_mm9/chr16.bed
https://bacpacresources.org/download/wi1_mm9/chr17.bed
https://bacpacresources.org/download/wi1_mm9/chr18.bed
https://bacpacresources.org/download/wi1_mm9/chr19.bed
https://bacpacresources.org/download/wi1_mm9/chrX.bed
https://bacpacresources.org/download/wi1_mm9/chrY.bed
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