Journal: Molecular cell

Article Title: R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters

doi: 10.1016/j.molcel.2017.10.008

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-V5 Santa Cruz sc-83849-R Mouse monoclonal anti-NONO Santa Cruz sc-166702 Mouse monoclonal anti-β-Actin Sigma-Aldrich A2228 Mouse monoclonal anti-RNAPII EMD Millipore 05-623-Z Mouse monoclonal S9.6 antibody Kerafast ENH001 Chemicals, Peptides, and Recombinant Proteins SIGMAFAST Protease Inhibitor Cocktail Tablets Sigma-Aldrich S8830-2TAB Glycogen Thermo Fisher FERR0561 Formaldehyde Sigma-Aldrich 252549-100ML Protein A/G magnetic beads Thermo Fisher PI88802 Proteinase K NEB P8107S RiboLock RNase inhibitor Thermo Fisher FEREO0382 RNase A Thermo Fisher EN0531 Phi29 DNA polymerase NEB M0269S Klenow Fragment (3′–5′ exo-) NEB M0212S T4 DNA ligase NEB M0202S FastStart Universal SYBR Green Master (ROX) 2X Roche 4913850001 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) Sigma-Aldrich D1916-50MG Br-UTP Sigma-Aldrich B7166-5MG M6101 RQ1 RNase-Free DNase Promega M6101 Antarctic Phosphatase NEB M0289S BrdU antibody conjugated agarose beads Santa Cruz sc-32323 AC T4 Polynucleotide Kinase NEB M0201S E. coli Poly(A) Polymerase NEB M0276S SuperScript III First-Strand Synthesis System Thermo Fisher 18080051 Exonuclease I NEB M0293S Circligase II Epicentre CL9021K APE 1 NEB M0282S Phusion High-Fidelity DNA Polymerase NEB M0530S SYBR Gold Nucleic Acid Gel Stain Thermo Fisher S-11494 HindIII-HF NEB R3104S BsrGI-HF NEB R3575S XbaI NEB R0145S SspI-HF NEB R3132S RNase H NEB M0297S Critical Commercial Assays PureLink PCR Micro Kit Thermo Fisher K310050 PureLink Quick Gel Extraction Kit Thermo Fisher K210012 Deposited Data Sequencing data of R-ChIP experiments This study GEO: {"type":"entrez-geo","attrs":{"text":"GSE97072","term_id":"97072"}} GSE97072 Sequencing data of GRO-seq experiments This study GEO: {"type":"entrez-geo","attrs":{"text":"GSE97072","term_id":"97072"}} GSE97072 Experimental Models: Cell Lines Human: HEK293T cells Laboratory of Steve Dowdy N/A Human: K562 Cells ATCC CCL-243 Oligonucleotides Primers for R-ChIP-qPCR and ChIP-qPCR experiments This study See Table S2 Software and Algorithms Bowtie2 Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Samtools Li et al., 2009 http://samtools.sourceforge.net/ Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/ R N/A https://www.r-project.org/ Ngsplot Shen et al., 2014 https://github.com/shenlab-sinai/ngsplot Deeptools Ramirez et al., 2014 http://deeptools.readthedocs.io/en/latest/ Step One Software v2.3 Thermo Fischer https://www.thermofisher.com/de/de/home/technicalresources/software-downloads/StepOne-and-StepOnePlus-Real-Time-PCR-System.html Open in a separate window KEY RESOURCES TABLE

Techniques: Recombinant, Protease Inhibitor, Magnetic Beads, SYBR Green Assay, Staining, Gel Extraction, Sequencing, Software