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The reads were then aligned to the mm9 build of the mouse genome using BSmap32.
We aligned these reads to the mm10 build of the mouse genome using TopHat version 2 (ref. 37).
Sequencing reads were aligned to the mm10 reference mouse genome using Bowtie273 and analyzed with HOMER31 for peak finding, motif analysis and peaks annotation.
Sequence reads were trimmed to remove any adapter sequences using Cutadapt version 1.8.350 then aligned to version GRCm38 of the mouse genome using HISAT251.
CRISPR guide RNAs (sgRNA) were designed to target the SCF gene kitl located on chromosome 10 of the mouse genome using the sgRNA scorer 2.0 and candidates were selected based on their high predicted activity and lack of off-target effects.
The ability to create targeted mutations in the mouse genome using homologous recombination in embryonic stem cells (gene targeting) has proved to be an extremely useful experimental approach.
In his lab, Perry and his team edited the mouse genome using what are essentially "molecular scissors".
The sequence was amplified from the mouse genome using primers listed in Table S1.
The ULTRA was amplified from the mouse genome using appropriate primers (Table S1).
The obtained sequences were then mapped to mouse genome using UCSC genome browser for splice junction analyses.
We sequenced the ChIP DNA with an Illumina Genome Analyzer and aligned the sequence reads to the mouse genome using Illumina's ELAND program.
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