Journal: Molecular cell

Article Title: Dynamic Processing of Displacement Loops during Recombinational DNA Repair

doi: 10.1016/j.molcel.2019.01.005

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Myc (9E11) Santa Cruz Biotechnology sc-47694, lot F11 13; RRID: AB_627266 Mouse monoclonal anti-GAPDH Thermo Scientific MA5–15738, lot QG215126; RRID: AB_10977387 Chemicals, Peptides, and Recombinant Proteins Trioxsalen (TMP) Sigma-Aldrich Cat#T6137 lndole-3-acetic acid (IAA) sodium salt (Auxin) Sigma-Aldrich Cat#l5148 dCTP-alpha-P32 6000 uCi/mmol PerkinElmer Cat#BLU-513Z T4 DNA Ligase New England Biolabs Cat#M0202 EcoRI-HF New England Biolabs Cat#R3101 Hindlll-HF New England Biolabs Cat#R3104 Critical Commercial Assays LightCycler 480 SYBR Green I Master Roche Life Science Cat#04707516001 Ambion DecaPrime II DNA labeling kit Thermo Fisher Cat#AM1455 Experimental Models: Organisms/Strains Saccharomyces cerevisiae; Individual genotypes see Table S1 This study N/A Oligonucleotides Quantitative PCR primers, see Table S2 Eurofins Genomics N/A Hybridization oligonucleotides, see Table S2 Sigma-Aldrich N/A Software and Algorithms LightCycler 480 Software Roche Life Science Cat#04994884001 R ×64 3.2.0 R Project https://www.r-project.org/ Ape Plasmid Editor Wayne Davis https://biologylabs.utah.edu/jorgensen/wayned/ape/ ImageJ 1.51k Wayne Rasband https://imagej.nih.gov/ij/ Other Spectrolinker (with 365 nm UV bulbs) Spectroline XL-1500 Open in a separate window KEY RESOURCES TABLE Development of a physical assay for D-loop detection in cells Srs2, Mph1, and Sgs1-Top3-Rmi1 (STR) regulate D-loop levels in vivo Two distinct pathways (Srs2 and Mph1, STR) target different D-loop species Rdh54 delineates the two D-loop reversal pathways

Techniques: Recombinant, SYBR Green Assay, DNA Labeling, Real-time Polymerase Chain Reaction, Hybridization, Software, Plasmid Preparation

Journal: FEMS microbiology letters

Article Title: Genome size and macrorestriction map of Xanthomonas campestris pv. glycines YR32 chromosome.

doi: 10.1111/j.1574-6968.1999.tb13602.x

Figure Lengend Snippet: Fig. 1. Pulsed-¢eld gel electrophoresis (PFGE) of X. campestris pv. glycines YR32 genomic DNA digested with PacI, SwaI, and PmeI (50^650-s pulse, 50-h run). A: PacI, SwaI and PacI-SwaI digestion. Lanes: 1, yeast chromosomal standards; 2, X. campestris pv. glycines YR32 genomic DNA digested with PacI; 3, PacI-SwaI digest; 4, SwaI digest; 5, R. sphaeroides 2.4.1 genomic DNA digested with SpeI as molecular size markers. B: PmeI, SwaI and PmeI-SwaI digestion. Lanes: 1, yeast chromosomal standards; 2, PmeI digest; 3, PmeI-SwaI digest; 4, SwaI digest; 5, SpeI-digested R. sphaeroides 2.4.1 markers. C: PacI, PmeI and Pac-PmeI digestion. Lanes: 1, yeast chromoso- mal standards; 2, PacI digest; 3, PacI-PmeI digest; 4, PmeI digest; 5, SpeI-digested R. sphaeroides 2.4.1 markers.

Article Snippet: For AseI and SpeI digests, lambda concatemeric DNA (New England Biolabs) and AseI-digested R. sphaeroides 2.4.1 genomic DNA [26] were used as a molecular size standards.

Techniques: Nucleic Acid Electrophoresis

Journal: FEMS microbiology letters

Article Title: Genome size and macrorestriction map of Xanthomonas campestris pv. glycines YR32 chromosome.

doi: 10.1111/j.1574-6968.1999.tb13602.x

Figure Lengend Snippet: Fig. 2. PFGE of X. campestris pv. glycines YR32 genomic DNA digested with AseI and SpeI. A: Optimal separation of the larg- est DNA fragments (25^70-s pulse, 24-h run, 180 V). Lanes: 1, concatemeric lambda DNA; 2, R. sphaeroides 2.4.1 genomic DNA digested with AseI as molecular size markers; 3, X. cam- pestris pv. glycines YR32 genomic DNA digested with AseI; 4, SpeI digest; 5, yeast chromosomal standards. B: Optimal separa- tion of small- and medium-sized DNA fragments (20^25-s pulse, 22-h run, 180 V). Lanes: 1, AseI-digested R. sphaeroides 2.4.1 markers; 2, X. campestris pv. glycines YR32 digested with SpeI; 3, AseI digest.

Article Snippet: For AseI and SpeI digests, lambda concatemeric DNA (New England Biolabs) and AseI-digested R. sphaeroides 2.4.1 genomic DNA [26] were used as a molecular size standards.

Techniques: Lambda DNA Preparation

Journal: FEMS microbiology letters

Article Title: Genome size and macrorestriction map of Xanthomonas campestris pv. glycines YR32 chromosome.

doi: 10.1111/j.1574-6968.1999.tb13602.x

Figure Lengend Snippet: Fig. 4. Southern hybridization using the pat gene as a probe. A: PFGE of X. campestris pv. glycines YR32 genomic DNA digested with PacI, PmeI, SwaI and multiple digests. Lanes: 1, R. sphaeroides 2.4.1 genomic DNA digested with SpeI as molecular size markers; 2, X. campestris pv. glycines YR32 genomic DNA digested with PacI; 3, PmeI digest; 4, SwaI digest; 5, PacI-PmeI digest; 6, PmeI-SwaI di- gest; 7, PacI-SwaI digest; 8, yeast chromosomal standards. B: Southern hybridization result.

Article Snippet: For AseI and SpeI digests, lambda concatemeric DNA (New England Biolabs) and AseI-digested R. sphaeroides 2.4.1 genomic DNA [26] were used as a molecular size standards.

Techniques: Hybridization

Journal: FEMS microbiology letters

Article Title: Genome size and macrorestriction map of Xanthomonas campestris pv. glycines YR32 chromosome.

doi: 10.1111/j.1574-6968.1999.tb13602.x

Figure Lengend Snippet: Fig. 5. PFGE of X. campestris pv. glycines YR32 digested with I-CeuI and subsequent digestion with PacI, PmeI, and SwaI. Lanes: 1, R. sphaeroides 2.4.1 genomic DNA digested with SpeI as molecular size markers; 2, I-CeuI digest; 3, I-CeuI-PacI di- gest; 4, I-CeuI-PmeI digest; 5, I-CeuI-SwaI digest; 6, I-CeuI- PacI-PmeI digest; 7, I-CeuI-PmeI-SwaI digest; 8, I-CeuI-PacI- SwaI digest; 9, yeast chromosomal standards.

Article Snippet: For AseI and SpeI digests, lambda concatemeric DNA (New England Biolabs) and AseI-digested R. sphaeroides 2.4.1 genomic DNA [26] were used as a molecular size standards.

Techniques: