Preparation of Murine Exome and Whole-Genome Libraries
Exome libraries and whole-genome libraries were prepared using a modified protocol49 (link). Modifications included: the use of 1,000 ng of treated gDNA, performing only six cycles of PCR amplification and usage of the Agilent SureSelectXT Mouse All Exon Kit for exon target capture. For murine WGS, after adapter ligation, libraries were only amplified by two cycles of PCR. Equimolar quantities of the whole-genome indexed libraries were multiplexed, with 18 libraries per pool. Results from 13 of the 18 libraries were used in our analysis. All pooled libraries were sequenced on an Illumina NovaSeq6000 using the 150-base pair (bp) paired-end format.
Perelli L., Carbone F., Zhang L., Huang J.K., Le C., Khan H., Citron F., Del Poggetto E., Gutschner T., Tomihara H., Soeung M., Minelli R., Srinivasan S., Peoples M., Lam T.N., Lundgren S., Xia R., Zhu C., Mohamed A.M., Zhang J., Sircar K., Sgambato A., Gao J., Jonasch E., Draetta G.F., Futreal A., Bakouny Z., Van Allen E.M., Choueiri T., Signoretti S., Msaouel P., Litchfield K., Turajlic S., Wang L., Chen Y.B., Di Natale R.G., Hakimi A.A., Giuliani V., Heffernan T.P., Viale A., Bristow C.A., Tannir N.M., Carugo A, & Genovese G. (2023). Interferon signaling promotes tolerance to chromosomal instability during metastatic evolution in renal cancer. Nature Cancer, 4(7), 984-1000.
Base pairExome Exon Genome librariesLigation Mouse Murine
Corresponding Organization : The University of Texas MD Anderson Cancer Center
Other organizations :
Martin Luther University Halle-Wittenberg, Università Cattolica del Sacro Cuore, Dana-Farber Cancer Institute, Baylor College of Medicine, The Francis Crick Institute, Memorial Sloan Kettering Cancer Center
Usage of the Agilent SureSelectXT Mouse All Exon Kit for exon target capture
Amplification of whole-genome libraries by two cycles of PCR
dependent variables
Sequencing results from 13 of the 18 libraries
control variables
Equimolar quantities of the whole-genome indexed libraries were multiplexed, with 18 libraries per pool
controls
No positive or negative controls were explicitly mentioned in the provided information.
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