Journal: Cell

Article Title: The DEAD-box protein Dhh1p couples mRNA decay and translation by monitoring codon optimality

doi: 10.1016/j.cell.2016.08.053

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-HA Biolegend Cat#901503; RRID:AB_2565005 Mouse monoclonal anti-PAB1 EnCor Biotechnology Cat#MCA-1G1; RRID:AB_2572370 Mouse monoclonal anti-GAPDH Cell Biolabs Cat#AKR-001 Chemicals, Peptides, and Recombinant Proteins Cycloheximide Sigma-Aldrich C1988; CAS: 66-81-9 Heparin Sigma-Aldrich H3393; CAS: 9041-08-1 SuperaseIn Ambion AM2694 RNase I Ambion AM2294 T4 Polynucleotide Kinase New England Biosciences M0201L T4 RNA Ligase 2, Truncated New England Biosciences M0242L Superscript III Invitrogen 56575 GlycoBlue ThermoFisher AM9515 Streptavidin Dynabeads Invitrogen 65002 Protease Inhibitor Cocktail Sigma-Aldrich P8215 Sepharose 6B beads Sigma-Aldrich 6B100 IgG Sepharose 6 Fast Flow GE Healthcare 17-0969-01 AcTEV-protease Invitrogen 12575-015 Calmodulin Sepharose GE Healthcare 17-0529-01 Critical Commercial Assays Ribo-Zero Gold rRNA Removal Kit (Yeast) Illumina MRZY1306 CircLigase ssDNA Ligase Epicentre CL4115K Deposited Data Raw and analyzed data This paper GEO: {"type":"entrez-geo","attrs":{"text":"GSE81269","term_id":"81269"}} GSE81269 Dhh1p CLIP Sequencing Mitchell et al, 2013 GEO: {"type":"entrez-geo","attrs":{"text":"GSE46142","term_id":"46142"}} GSE46142 R64-1-1 S288C sacCer3 Genome Assembly Saccharomyces Genome Database Project http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/ Yeast ncRNA Gene Database Saccharomyces Genome Database Project http://downloads.yeastgenome.org/sequence/S288C_reference/rna/archive/rna_coding_R64-1-1_20110203.fasta.gz Experimental Models: Cell Lines Experimental Models: Organisms/Strains See Table S2 for a list of strains used in this study This paper N/A Recombinant DNA See Table S4 for a list of plasmids used in this study This paper N/A Sequence-Based Reagents See Table S3 for a list of oligonucleotides used in this study This paper N/A Software and Algorithms Bowtie Langmead et al., 2009 http://bowtie-bio.sourceforge.net ImageQuant GE Healthcare TL 5.2 ImageJ NIH, USA http://imagej.nih.gov/ij CutAdapt Martin, 2011 https://cutadapt.readthedocs.io/en/stable/ Other Analysis and scripts of deep sequencing data (Pipeline.py, DataGen.py, Plot.R) This paper https://github.com/greenlabjhmi/2016-Cell-Dhh1 Open in a separate window KEY RESOURCES TABLE

Techniques: Recombinant, Protease Inhibitor, Sequencing, Software