Journal: Molecular cell

Article Title: An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors

doi: 10.1016/j.molcel.2021.01.013

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-GFP Abcam ab290; RRID: AB_303395 Chemicals, peptides, and recombinant proteins Corticosterone Sigma-Aldrich Cat# 27840; CAS: 50-22-6 Dexamethasone Sigma-Aldrich D1756; CAS: 50-02-2 16% Paraformaldehyde (formaldehyde) aqueous solution Electron Microscopy Sciences 15710; CAS: 30525-89-4 8% Aqueous Solution Glutaraldehyde Electron Microscopy Sciences Cat# 16000 Tetracycline Sigma-Aldrich T7660; CAS: 60-54-8 JF549 HaloTag ligand Grimm et al., 2015 N/A PA-JF549 HaloTag ligand Grimm et al., 2016 N/A Critical commercial assays TruSeq Chip Sample Prep Kit Illumina IP-202-1012 Nextera DNA Library Prep Kit Illumina FC-121-1030 Magna ChIP Protein A+G Magnetic Beads Millipore-Sigma 16-663 Deposited data Raw sequencing data generated This paper GEO: {"type":"entrez-geo","attrs":{"text":"GSE154771","term_id":"154771"}} GSE154771 Sample of raw datasets of SMT imaging This paper https://doi.org/10.17632/k6g3xtr5k5.1 GR ChIP-seq and Atac-seq from 3617GRKO-GPFGR cells Paakinaho et al., 2019 GEO: {"type":"entrez-geo","attrs":{"text":"GSE108634","term_id":"108634"}} GSE108634 Experimental models: cell lines 3617 cells Paakinaho et al., 2017 N/A GRKO cells with stably integrated HaloTag-GR Paakinaho et al., 2017 N/A GRKO cells with stably integrated GFP-GRwt Paakinaho et al., 2019 N/A GRKO cells with stably integrated GFP-GR407C This paper N/A GRKO cells with stably integrated GFP-GR428G This paper N/A Recombinant DNA gRNA-pX330 SpCas9 ( Cong et al., 2013 ) Addgene #42230 Donor-Rosa_Puro_CMV_01292016 Paakinaho et al., 2019 N/A pHaloTag-GR Morisaki et al., 2014 N/A pHaloTag-H2B Mazza et al., 2012 N/A pHalo-PPARα Promega FHC03156 pHaloTag-GRdim This paper N/A pHaloTag-GRmon This paper N/A pHaloTag-GR407C This paper N/A pHaloTag-GR440C Paakinaho et al., 2017 N/A pGFP-GRwt Paakinaho et al., 2019 N/A pGFP-GR407C This paper N/A pGFP-GRC428G This paper N/A pGPF-NF1 Presman et al., 2017 N/A Software and Algorithms Trimmomatic 0.36 Bolger et al., 2014 http://www.usadellab.org/cms/?page=trimmomatic ; RRID: SCR_011848 SAMTools Li et al., 2009 https://github.com/samtools/samtools BEDTools Quinlan and Hall, 2010 https://github.com/arq5x/bedtools2 ; RRID: SCR_006646 Bowtie2 Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ; RRID:SCR_005476 HOMER 4.9 Heinz et al., 2010 http://homer.ucsd.edu/homer/ ; RRID: SCR_010881 MATLAB The MathWorks, Inc https://www.mathworks.com/products/matlab.html TrackRecord Mazza et al., 2013 and Garcia et al., 2020 https://github.com/davidalejogarcia/PL_HagerLab Custom MATLAB code Garcia et al., 2020 https://github.com/davidalejogarcia/PL_HagerLab Open in a separate window KEY RESOURCES TABLE

Techniques: Recombinant, Electron Microscopy, Sample Prep, Magnetic Beads, Sequencing, Generated, Imaging, Stable Transfection, Software

Journal: Molecular cell

Article Title: An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors

doi: 10.1016/j.molcel.2021.01.013

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-GFP Abcam ab290; RRID: AB_303395 Chemicals, peptides, and recombinant proteins Corticosterone Sigma-Aldrich Cat# 27840; CAS: 50-22-6 Dexamethasone Sigma-Aldrich D1756; CAS: 50-02-2 16% Paraformaldehyde (formaldehyde) aqueous solution Electron Microscopy Sciences 15710; CAS: 30525-89-4 8% Aqueous Solution Glutaraldehyde Electron Microscopy Sciences Cat# 16000 Tetracycline Sigma-Aldrich T7660; CAS: 60-54-8 JF549 HaloTag ligand Grimm et al., 2015 N/A PA-JF549 HaloTag ligand Grimm et al., 2016 N/A Critical commercial assays TruSeq Chip Sample Prep Kit Illumina IP-202-1012 Nextera DNA Library Prep Kit Illumina FC-121-1030 Magna ChIP Protein A+G Magnetic Beads Millipore-Sigma 16-663 Deposited data Raw sequencing data generated This paper GEO: {"type":"entrez-geo","attrs":{"text":"GSE154771","term_id":"154771"}} GSE154771 Sample of raw datasets of SMT imaging This paper https://doi.org/10.17632/k6g3xtr5k5.1 GR ChIP-seq and Atac-seq from 3617GRKO-GPFGR cells Paakinaho et al., 2019 GEO: {"type":"entrez-geo","attrs":{"text":"GSE108634","term_id":"108634"}} GSE108634 Experimental models: cell lines 3617 cells Paakinaho et al., 2017 N/A GRKO cells with stably integrated HaloTag-GR Paakinaho et al., 2017 N/A GRKO cells with stably integrated GFP-GRwt Paakinaho et al., 2019 N/A GRKO cells with stably integrated GFP-GR407C This paper N/A GRKO cells with stably integrated GFP-GR428G This paper N/A Recombinant DNA gRNA-pX330 SpCas9 ( Cong et al., 2013 ) Addgene #42230 Donor-Rosa_Puro_CMV_01292016 Paakinaho et al., 2019 N/A pHaloTag-GR Morisaki et al., 2014 N/A pHaloTag-H2B Mazza et al., 2012 N/A pHalo-PPARα Promega FHC03156 pHaloTag-GRdim This paper N/A pHaloTag-GRmon This paper N/A pHaloTag-GR407C This paper N/A pHaloTag-GR440C Paakinaho et al., 2017 N/A pGFP-GRwt Paakinaho et al., 2019 N/A pGFP-GR407C This paper N/A pGFP-GRC428G This paper N/A pGPF-NF1 Presman et al., 2017 N/A Software and Algorithms Trimmomatic 0.36 Bolger et al., 2014 http://www.usadellab.org/cms/?page=trimmomatic ; RRID: SCR_011848 SAMTools Li et al., 2009 https://github.com/samtools/samtools BEDTools Quinlan and Hall, 2010 https://github.com/arq5x/bedtools2 ; RRID: SCR_006646 Bowtie2 Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ; RRID:SCR_005476 HOMER 4.9 Heinz et al., 2010 http://homer.ucsd.edu/homer/ ; RRID: SCR_010881 MATLAB The MathWorks, Inc https://www.mathworks.com/products/matlab.html TrackRecord Mazza et al., 2013 and Garcia et al., 2020 https://github.com/davidalejogarcia/PL_HagerLab Custom MATLAB code Garcia et al., 2020 https://github.com/davidalejogarcia/PL_HagerLab Open in a separate window KEY RESOURCES TABLE

Techniques: Recombinant, Electron Microscopy, Sample Prep, Magnetic Beads, Sequencing, Generated, Imaging, Stable Transfection, Software