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Methods: Multiplexed profiling of candidate genes for CpG island methylation status using a flexible PCR/LDR/Universal Array assay
- Yu-Wei Cheng,
- Carrie Shawber,
- Dan Notterman,
- Philip Paty,
- and Francis Barany
Genome Res. February 2006 16: 282-289; Published in Advance December 20, 2005, doi:10.1101/gr.4181406
.... Overall, our data demonstrate that bisulfite-PCR/LDR/Universal Array approach is a quantitative and sensitive method for the measurement of DNA methylation. View larger version: In this window In a new window Figure 3. The quantification curves of the assay. Genomic DNAs of HCT15 and normal human...
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GENOME METHODS: A Homogeneous, Ligase-Mediated DNA Diagnostic Test
- Xiangning Chen,
- Kenneth J. Livak,
- and Pui-Yan Kwok
Genome Res. May 1, 1998 8: 549-556; doi:10.1101/gr.8.5.549
...the development of a homogeneous DNA detection method that requires no further manipulations after the initial reaction is set up. This assay, named dye-labeled oligonucleotide ligation (DOL), combines the PCR and the oligonucleotide ligation reaction in a two-stage thermal cycling sequence with fluorescence...
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Method: Quantification of somatic mutation flow across individual cell division events by lineage sequencing
- Yehuda Brody,
- Robert J. Kimmerling,
- Yosef E. Maruvka,
- David Benjamin,
- Juniper J. Elacqua,
- Nicholas J. Haradhvala,
- Jaegil Kim,
- Kent W. Mouw,
- Kristjana Frangaj,
- Amnon Koren,
- Gad Getz,
- Scott R. Manalis,
- and Paul C. Blainey
Genome Res. December 2018 28: 1901-1918; Published in Advance November 20, 2018, doi:10.1101/gr.238543.118
...subclonal cultures representing individual lineages. From our time-lapse data, we were able to measure the inter-division times for all cells in the device. We extracted genomic DNA from subclones and prepared PCR-free shotgun sequence libraries, which were sequenced to 35-fold coverage (Methods...
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Research: Sequence determinants of improved CRISPR sgRNA design
- Han Xu,
- Tengfei Xiao,
- Chen-Hao Chen,
- Wei Li,
- Clifford A. Meyer,
- Qiu Wu,
- Di Wu,
- Le Cong,
- Feng Zhang,
- Jun S. Liu,
- Myles Brown,
- and X. Shirley Liu
Genome Res. August 2015 25: 1147-1157; Published in Advance June 10, 2015, doi:10.1101/gr.191452.115
...isolation of the DNA and proteins.SURVEYOR nuclease assay and Western blotThe DNA fragments of the AASV1 locus were amplified from extracted genomic DNA by PCR using the Q5 high-fidelity DNA polymerases (NEB). SURVEYOR nuclease assays were subsequently performed according to the manufacturer's instructions...
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Resource: Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis
- Chirag Nepal,
- Yavor Hadzhiev,
- Christopher Previti,
- Vanja Haberle,
- Nan Li,
- Hazuki Takahashi,
- Ana Maria M. Suzuki,
- Ying Sheng,
- Rehab F. Abdelhamid,
- Santosh Anand,
- Jochen Gehrig,
- Altuna Akalin,
- Christel E.M. Kockx,
- Antoine A.J. van der Sloot,
- Wilfred F.J. van IJcken,
- Olivier Armant,
- Sepand Rastegar,
- Craig Watson,
- Uwe Strähle,
- Elia Stupka,
- Piero Carninci,
- Boris Lenhard,
- and Ferenc Müller
Genome Res. November 2013 23: 1938-1950; Published in Advance September 3, 2013, doi:10.1101/gr.153692.112
...is shown as reference for view of fluorescence image. Nepal et al . 1944 Genome Research www..org These data, together with the independent developmental dynamics, cDNA alignment, and reporter gene functional assays, argue that exon and intron 59- and 39-end associated RNAs are biochemically independent...

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