Journal: Molecular cell

Article Title: In vivo evidence for ATPase-dependent DNA translocation by the Bacillus subtilis SMC condensin complex

doi: 10.1016/j.molcel.2018.07.006

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-SMC polyclonal rabbit antibody ( Lindow et al., 2002 ) N/A Anti-ParB polyclonal rabbit antibody ( Lin et al., 1997 ) N/A Anti-ScpA polyclonal rabbit antibody, affinity purified ( Wang et al., 2017 ) N/A Anti-ScpA polyclonal rabbit antibody, affinity purified ( Wang et al., 2017 ) N/A Anti-SigA polyclonal rabbit antibody ( Fujita, 2000 ) N/A Chemicals, Peptides, and Recombinant Proteins Benzonase EMD Cat # 7046 Ni-NTA agarose Qiagen Cat # 30230 HiTrap Q HP GE Healthcare Cat # 17115301 Bradford Assay Kit ThermoFisher Cat # 23236 ATP Dot Scientific Cat # DSA30030–5 NADH Acros Organic Cat # 271100010 Phosphoenolypyruvate Tokyo Chemical Industry Cat # P0256 Rabbit Pyruvate Kinase Roche Diagnostics Cat # 10109045001 Lactate Dehydrogenase Sigma, Darmstadt, Germany Cat # L2500–25KU Formaldehyde 37% Sigma Cat # F8775 Ready-Lyse Lysozyme Epicentre Cat # R1802M HindIII NEB Cat # R0104M Klenow NEB Cat # M0210L Biotin-14-dATP ThermoFisher Cat # 19524016 T4 DNA ligase NEB Cat # M0202M Proteinase K NEB Cat # P8107S T4 DNA Polymerase NEB Cat # M0203L Critical Commercial Assays ATPase/GTPase Activity Assay Kit Sigma Cat # MAK113 NEBNext Ultra II DNA Library Prep Kit NEB Cat # E7645S Deposited Data Raw and analyzed Hi-C data This paper GEO: {"type":"entrez-geo","attrs":{"text":"GSE95137","term_id":"95137"}} GSE95137 Original Data Mendeley Data http://dx.doi.org/10.17632/tygwp234gr.1 Experimental Models: Organisms/Strains Bacillus subtilis strains, see Table S1 Oligonucleotides See Table S3 Recombinant DNA See Table S2 Software and Algorithms MATLAB 8.5 (R2015) ( Wang et al., 2017 ) https://www.mathworks.com/ hiclib ( Imakaev et al., 2012 ) https://bitbucket.org/mirnylab/hiclib Open in a separate window KEY RESOURCES TABLE

Techniques: Affinity Purification, Recombinant, Bradford Assay, Activity Assay, Software

Journal: Cell

Article Title: Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

doi: 10.1016/j.cell.2019.01.020

Figure Lengend Snippet: HIGHLIGHTS

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Critical Commercial Assays Deposited Data HFF-hTERT dilution Hi-C This paper 4DN: 4DNES9L4AK6Q HFF-hTERT clone 6 in-situ Hi-C 4D Nucleome 4DN: 4DNES2R6PUEK Rao et al in-situ Hi-C Rao et al., 2013 {"type":"entrez-geo","attrs":{"text":"GSE74072","term_id":"74072"}} GSE74072 Jin et al dilution Hi-C Jin et al., 2013 {"type":"entrez-geo","attrs":{"text":"GSE85977","term_id":"85977"}} GSE85977 FISH spot positions and distances This paper 4DN: https://data.4dnucleome.org/publications/80007b23-7748-4492-9e49-c38400acbe60/ Experimental Models: Cell Lines HFF-hTERT cells 4D Nucleome RRID: CVCL_VC40 Experimental Models: Organisms/Strains Oligonucleotides Recombinant DNA BAC clones (See Table S1 ) CHORI See Table S1 Software and Algorithms Bowtie2.2.8 Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Hiclib Imakaev et al., 2012 https://bitbucket.org/mirnylab/hiclib Cooler Abdennur et al, 2017 http://doi.org/10.5281/zenodo.1039971 Lavaburst (domain calling algorithms) Schwarzer et al, 2017 https://github.com/nvictus/lavaburst cWorld Lajoie et al., 2015 https://github.com/dekkerlab/cworld-dekker Other Open in a separate window HIGHLIGHTS Genome organization is highly variable between individual cells.

Techniques: Virus, Recombinant, Clone Assay, Software

Journal: Cell

Article Title: A pliable Mediator acts as a functional rather than an architectural bridge between promoters and enhancers

doi: 10.1016/j.cell.2019.07.011

Figure Lengend Snippet: (A) Genetic screen from mouse T, B and ES cells compared to yeast and the hMED minimal core. Essential subunits denoted with red boxes, non-essential with grey ones, minimal core subunits with checkmarks. (B) Bar graph shows the number of transcriptionally affected genes (>1.5 fold) in CH12 B cells deficient for non-essential (non-tail) mMED subunits. (C) Schematic showing MED14-degron strategy. A SMASh tag consisting of a linker, the hepatitis C protease, and a degron subunit was fused to MED14-N terminus. In untreated cells, the protease frees MED14 from SMASh, which is degraded. The hepatitis C protease inhibitor Asunaprevir blocks SMASh cleavage leading to MED14 degradation. (D) Transcriptome analysis of APR-treated Med14SMASh vs. control cells. Red dots represent mRNA spike-ins used to normalize signals on a per cell basis. (E) Med26, PolII, PolII-S5, PolII-S2, H3K4me3, H3K4me1, and H3K27Ac ChIP-Seq profiles at the Xbp1 locus in APR-treated WT (left) or Med14SMASh (right) cells. The orientation of genes is denoted with red arrows.

Article Snippet: Antibody SOURCE IDENTIFIER Tested Cell Remark Med1 Bethyl A300–793A aB Not worked Med6 Origene TA343540 CH12 Not worked Med12 Bethyl A300–774A aB, CH12 Very low signal-to-noise ratio Med14 Abcam ab170605 CH12 Not worked Med14 Thermo Fisher PA5–44864 CH12 Not worked Med19 Abcam ab179735 CH12 low signal-to-noise ratio Med23 Bethyl A300–425A aB, CH12 Good quality Med24 Novus Biologicals NB100–92293 aB low signal-to-noise ratio Med25 Thermo Fisher PA5–43616 aB low signal-to-noise ratio Med26 Cell Signaling 13641S CH12 Good quality Cdk8 Abcam ab176559 CH12 low signal-to-noise ratio Open in a separate window In situ HiC We generated 34 in situ Hi-C libraries using the MboI restriction enzyme.

Techniques: Protease Inhibitor, ChIP-sequencing

Journal: Cell

Article Title: A pliable Mediator acts as a functional rather than an architectural bridge between promoters and enhancers

doi: 10.1016/j.cell.2019.07.011

Figure Lengend Snippet:

Article Snippet: Antibody SOURCE IDENTIFIER Tested Cell Remark Med1 Bethyl A300–793A aB Not worked Med6 Origene TA343540 CH12 Not worked Med12 Bethyl A300–774A aB, CH12 Very low signal-to-noise ratio Med14 Abcam ab170605 CH12 Not worked Med14 Thermo Fisher PA5–44864 CH12 Not worked Med19 Abcam ab179735 CH12 low signal-to-noise ratio Med23 Bethyl A300–425A aB, CH12 Good quality Med24 Novus Biologicals NB100–92293 aB low signal-to-noise ratio Med25 Thermo Fisher PA5–43616 aB low signal-to-noise ratio Med26 Cell Signaling 13641S CH12 Good quality Cdk8 Abcam ab176559 CH12 low signal-to-noise ratio Open in a separate window In situ HiC We generated 34 in situ Hi-C libraries using the MboI restriction enzyme.

Techniques: