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Method: Application of microdroplet PCR for large-scale targeted bisulfite sequencing
- H. Kiyomi Komori,
- Sarah A. LaMere,
- Ali Torkamani,
- G. Traver Hart,
- Steve Kotsopoulos,
- Jason Warner,
- Michael L. Samuels,
- Jeff Olson,
- Steven R. Head,
- Phillip Ordoukhanian,
- Pauline L. Lee,
- Darren R. Link,
- and Daniel R. Salomon
Genome Res. October 2011 21: 1738-1745; Published in Advance July 14, 2011, doi:10.1101/gr.116863.110
...), 3.6 mL of 4M Betaine (Sigma), 3.6 mL of RDTDroplet Stabilizer (RainDance Technologies), 1.8 mL dimethyl sulfoxide (Sigma) and 0.7 mL of 5 U/mLPlatinumHigh-Fidelity Taq (Invitrogen). Sampleswerebrought to a final volume of 25mLwith nuclease free water (Teknova, Fisher). Droplet library construction...
ARTICLE: A comparison of methods for RNA extraction from lymphocytes for RT-PCR.
- W Liedtke,
- L Battistini,
- C F Brosnan,
- and C S Raine
Genome Res. December 1994 4: 185-187
.../ml. The cells were cryoconserved in RPMI 1640 containing 10% fetal calf serum and 30% dimethyl- sulfoxide (DMSO) (all reagents from Sigma, St. Louis, MO). Cells were either pelleted by centrifuging for 5 min at 12,000g or exposed to the lysis agent without centrifugation (volume 1:1). To estimate the effect...
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ARTICLES: Direct PCR sequencing of murine immunoglobulin genes using E. coli single-stranded DNA-binding protein.
- R Rapley,
- S Flora,
- and M R Walker
Genome Res. August 1992 2: 99-101; doi:10.1101/gr.2.1.99
...sequencing PCR amplified material using dimethyl sulphoxide. Nucleic Acids Res. 17 : 1266 . 3.. Bachmann, B., , Lucke, W. , Hunsmann. G. Bachmann, B., Lucke, W. and Hunsmann. G. 1990 . Improvement of PCR amplified DNA sequencing with the aid of detergents. Nucleic Acids Res. 18 : 1309 . 4.. Innis, M...
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ARTICLES: Effect of internal direct and inverted Alu repeat sequences on PCR.
- W Ji,
- X Y Zhang,
- G S Warshamana,
- G Z Qu,
- and M Ehrlich
Genome Res. October 1994 4: 109-116
...% dimethyl- sulfoxide, 10 -s or 10 -4 M tetramethyl- ammonium chloride) or the prediges- tion of the template DNA with a restric- tion endonuclease that cleaved only out- side the amplified region also did not appreciably decrease the formation of the in vitro deletion product from non- mutant human DNA...
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Research: The impact of SWI/SNF and NuRD inactivation on gene expression is tightly coupled with levels of RNA polymerase II occupancy at promoters
- Sachin Pundhir,
- Jinyu Su,
- Marta Tapia,
- Anne Meldgaard Hansen,
- James Seymour Haile,
- Klaus Hansen,
- and Bo Torben Porse
Genome Res. March 2023 33: 332-345; Published in Advance March 16, 2023, doi:10.1101/gr.277089.122
...of dimethyl sulfoxide (DMSO) as control for 3 h and directly fixed and subjected to ChIP.shRNA constructionTo generate Chd4 and scrambled shRNA constructs, PLKO.1 plasmid forward and reverse oligos were annealed to generate double-stranded Chd4 and scrambled shRNAs inserts containing AgeI- and Eco...
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Resource: Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis
- Leslie O. Goodwin,
- Erik Splinter,
- Tiffany L. Davis,
- Rachel Urban,
- Hao He,
- Robert E. Braun,
- Elissa J. Chesler,
- Vivek Kumar,
- Max van Min,
- Juliet Ndukum,
- Vivek M. Philip,
- Laura G. Reinholdt,
- Karen Svenson,
- Jacqueline K. White,
- Michael Sasner,
- Cathleen Lutz,
- and Stephen A. Murray
Genome Res. March 2019 29: 494-505; Published in Advance January 18, 2019, doi:10.1101/gr.233866.117
...mutagenesis at the integration site. Inverse PCR can be used to clone the actual fusion sequence but has a high failure rate owing to the multicopy nature of most transgenes. More recently, high-throughput sequencing (HTS) has been employed to identify transgene insertion sites (Dubose et al. 2013...
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Research: Targeted delivery of CRISPR interference system against Fabp4 to white adipocytes ameliorates obesity, inflammation, hepatic steatosis, and insulin resistance
- Jee Young Chung,
- Qurrat Ul Ain,
- Yoonsung Song,
- Seok-Beom Yong,
- and Yong-Hee Kim
Genome Res. September 2019 29: 1442-1452; Published in Advance August 29, 2019, doi:10.1101/gr.246900.118
...and ATS-9R at weight ratios of 4 and 5. After 24 h, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) solution was added to the media at 10% v/v and incubated for 4 h. Then, the medium was replaced with dimethyl sulfoxide and incubated for an additional 15 min. The absorbance of each...
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Research: Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma
- Winnie S. Liang,
- William Hendricks,
- Jeffrey Kiefer,
- Jessica Schmidt,
- Shobana Sekar,
- John Carpten,
- David W. Craig,
- Jonathan Adkins,
- Lori Cuyugan,
- Zarko Manojlovic,
- Rebecca F. Halperin,
- Adrienne Helland,
- Sara Nasser,
- Christophe Legendre,
- Laurence H. Hurley,
- Karthigayini Sivaprakasam,
- Douglas B. Johnson,
- Holly Crandall,
- Klaus J. Busam,
- Victoria Zismann,
- Valerie Deluca,
- Jeeyun Lee,
- Aleksandar Sekulic,
- Charlotte E. Ariyan,
- Jeffrey Sosman,
- and Jeffrey Trent
Genome Res. April 2017 27: 524-532; doi:10.1101/gr.213348.116
...until death from melanoma or date of last follow-up. Analysis was performed using SAS software (v9.4) (Supplemental Fig. S1A,B). TERT inhibitor viability experiments Cell lines were plated in 96-well microplates, in 100 µL culture medium. Twenty-four hours after plating cells, dimethyl sulfoxide (DMSO...
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Research: Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma
- Mauro Castellarin,
- René L. Warren,
- J. Douglas Freeman,
- Lisa Dreolini,
- Martin Krzywinski,
- Jaclyn Strauss,
- Rebecca Barnes,
- Peter Watson,
- Emma Allen-Vercoe,
- Richard A. Moore,
- and Robert A. Holt
Genome Res. February 2012 22: 299-306; Published in Advance October 18, 2011, doi:10.1101/gr.126516.111
..., and H, respectively. All strains were stored at −80°C in cryoprotectant media (12% [w/v] skim milk powder, 1% [v/v] dimethyl sulfoxide, and 1% [v/v] glycerol).Primer walkingPCR primers were designed using primer 3.0 and the F. nucleatum types strain (ATCC 25586) as reference. For PCR, 1 ng of extracted...
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Research: H2A.B facilitates transcription elongation at methylated CpG loci
- Yibin Chen,
- Qiang Chen,
- Richard C. McEachin,
- James D. Cavalcoli,
- and Xiaochun Yu
Genome Res. April 2014 24: 570-579; Published in Advance January 8, 2014, doi:10.1101/gr.156877.113
...polymerase (Promega) using 0.3 mM of each primer (Supplemental Table S2) and 0.1 mCi of [32P]dCTP. For region C of Kcnq1, Herculase DNA polymerase (Stratagene) was used for the PCR, with 13Herculase buffer, 0.3 mMof each primer, 0.8 mM deoxynucleoside triphosphates, 4% dimethyl sulfoxide, and 0.1 mCi of [32P...

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