Journal: Cell systems

Article Title: Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor Alpha Bound Enhancers

doi: 10.1016/j.cels.2017.08.011

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: DATA AND SOFTWARE AVAILABILITY Software: See Key Resources Table. table ft1 table-wrap mode="anchored" t5 caption a7 REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies H3K27ac rabbit polyclonal Active Motif Cat# 39133; RRID:AB_2561016 H3K9me3 rabbit polyclonal Abcam Cat# ab8898; RRID:AB_306848 FLAG mouse monoclonal Sigma-Aldrich Cat# F1804; RRID:AB_262044 RNA pol II 4H8 mouse monoclonal Abcam Cat# ab5408; RRID:AB_304868 ER alpha rabbit polyclonal Santa Cruz Cat#sc-544; RRID:AB_631469 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins β-estradiol Sigma-Aldrich Cat# E2758 Trichostatin A Cayman Chemicals Cat# 89730; CAS 58880-19-6 Critical Commercial Assays ZR 96-well Quick-RNA Zymo Research Cat# R1053 KAPA Stranded mRNA-seq KAPA Biosystems Cat# KK8420 Power SYBR® Green RNA-to-CT™ 1-Step Applied Biosystems Cat# 4389986 Deposited Data Raw and analyzed ChIP-seq data This study {"type":"entrez-geo","attrs":{"text":"GSE99906","term_id":"99906"}} GSE99906 Raw and analyzed RNA-seq data This study {"type":"entrez-geo","attrs":{"text":"GSE99906","term_id":"99906"}} GSE99906 Experimental Models: Cell Lines Human: Ishikawa cells ECACC ECACC Cat# 99040201, RRID:CVCL_2529 Experimental Models: Organisms/Strains Ishikawa SID4x-dCas9-KRAB This study Oligonucleotides gBlocks, see Table S1 Primers for constructing and verifying dCas9 fusions and guide RNAs, see Table S2 Guide RNA targets, see Table S3 qPCR primers, see Table S4 Primers for sequencing ERBS deletions, see Table S5 Recombinant DNA dCas9-VP160 Cheng et al., 2013 Addgene 48227 pGL3-U6-PGK-Puro Shen et al., 2014 Addgene 51133 gRNA_cloningVector Mali et al., 2013 Addgene 41824 Software and Algorithms Bowtie Langmead et al., 2009 DOI: 10.1186/gb-2009-10-3-r25 MACS2 Zhang et al., 2008 DOI: 10.1186/gb-2008-9-9-r137 DESeq2 Love et al., 2014 DOI: 10.1186/s13059-014-0550-8 HISAT Kim et al., 2015 DOI: 10.1038/nmeth.3317 HTSeq Anders et al., 2015 DOI: 10.1093/bioinformatics/btu638 Bedtools Quinlan and Hall, 2010 DOI: 10.1093/bioinformatics/btq033 Prism 6 http://www.graphpad.com/scientific-software/prism/ Other Open in a separate window KEY RESOURCES TABLE Data produced in this study are available from GEO ( {"type":"entrez-geo","attrs":{"text":"GSE99906","term_id":"99906"}} GSE99906 ).

Techniques: Recombinant, SYBR Green Assay, Sequencing, Software

Journal: Molecular Systems Biology

Article Title: A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X

doi: 10.1038/s44320-024-00013-0

Figure Lengend Snippet: Reagents and tools.

Article Snippet: For the RNA-seq, RNA was extracted from 25 μl intact lysate (non-digested) using the Direct-zol kit (Zymo Research) and stranded total RNA libraries were prepared using the TruSeq Stranded Total RNA Human/Mouse/Rat kit (Illumina), following manufacturer’s instructions.

Techniques: Sequencing, Software, Flow Cytometry, Staining, Real-time Polymerase Chain Reaction

Journal: Developmental cell

Article Title: Myocardial polyploidization creates a barrier to heart regeneration in zebrafish

doi: 10.1016/j.devcel.2018.01.021

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Quantitative real-time PCR RNA from cardiac ventricles or zebrafish larvae was extracted using Trizol reagent (Life Technologies) and the Direct-zol RNA MicroPrep kit (Zymo Research).

Techniques: Recombinant, RNAscope 2.5 HD Assay, TUNEL Assay, In Situ, Clone Assay, Software, Fluorsave, Plasmid Preparation

Journal: International Journal of Molecular Sciences

Article Title: A Liquid Biopsy in Bladder Cancer—The Current Landscape in Urinary Biomarkers

doi: 10.3390/ijms23158597

Figure Lengend Snippet: Table presenting data for methylation biomarkers.

Article Snippet: DNA hypermethylation (RASSF1, RARB, DAPK, TERT, APC) , diagnostic , n = 85 (BCa = 50, NMIBC = 37, MIBC = 5; control group = 35) , , Urine samples were collected form 85 patients before cystoscopy. DNA was extracted from urine using the Cells and Tissue DNA Isolation Kit (Norgen Biotek Corp., Thorold, Canada). Sodium bisulfite modification of DNA was performed with the EZ DNA Methylation-GoldKit (Zymo Research, Orange, CA). Quantification of the percentage of methylation of DNA was performed with Luna Universal Probe qPCR Master Mix (New England Biolabs, Ipswich, MA, USA) and on Applied Biosystems StepOnePlus Real Time PCR System (Thermo Fisher Scientific, Inc., Waltham, MA, USA). , BCa detection , , , , AUC = 0.76, PPV = 90%, NPV = 53%, Se. = 61.4%, Sp. = 86.4% , Prospective , [ ] .

Techniques: Methylation, Diagnostic Assay, Real-time Polymerase Chain Reaction, Isolation, DNA Methylation Assay, Software, DNA Extraction, Modification, Sequencing, Amplification

Journal: Expert Review of Molecular Diagnostics

Article Title: Recent advances in the diagnosis of COVID-19: a bird’s eye view

doi: 10.1080/14737159.2021.1874354

Figure Lengend Snippet: The common symptoms and clinical specimens taken from patients for diagnosis of SARS-CoV-2

Article Snippet: 25. , Quick SARS-CoV-2 rRT-PCR Kit (USA) by Zymo Research Corp/R3011/ [ ] , Bio-Rad CFX96 Touch and Applied Biosystems™ Quant Studio 5 Real-Time PCR Detection System, , N gene.

Techniques:

Journal: Expert Review of Molecular Diagnostics

Article Title: Recent advances in the diagnosis of COVID-19: a bird’s eye view

doi: 10.1080/14737159.2021.1874354

Figure Lengend Snippet: List of qRT-PCR kits approved by FDA (Food and Drug Administration)

Article Snippet: 25. , Quick SARS-CoV-2 rRT-PCR Kit (USA) by Zymo Research Corp/R3011/ [ ] , Bio-Rad CFX96 Touch and Applied Biosystems™ Quant Studio 5 Real-Time PCR Detection System, , N gene.

Techniques: Real-time Polymerase Chain Reaction, Software, Reverse Transcription Polymerase Chain Reaction, Luminex, Stripping Membranes, Multiplex Assay

Journal: Expert Review of Molecular Diagnostics

Article Title: Recent advances in the diagnosis of COVID-19: a bird’s eye view

doi: 10.1080/14737159.2021.1874354

Figure Lengend Snippet: CRISPR-based assays for rapid detection of SARS-CoV-2

Article Snippet: 25. , Quick SARS-CoV-2 rRT-PCR Kit (USA) by Zymo Research Corp/R3011/ [ ] , Bio-Rad CFX96 Touch and Applied Biosystems™ Quant Studio 5 Real-Time PCR Detection System, , N gene.

Techniques: CRISPR, Stripping Membranes, Binding Assay, Fluorescence, Lateral Flow Assay, Detection Assay

Journal: Expert Review of Molecular Diagnostics

Article Title: Recent advances in the diagnosis of COVID-19: a bird’s eye view

doi: 10.1080/14737159.2021.1874354

Figure Lengend Snippet: Summary of CRISPR-based assays being developed for the detection of SARS-CoV-2

Article Snippet: 25. , Quick SARS-CoV-2 rRT-PCR Kit (USA) by Zymo Research Corp/R3011/ [ ] , Bio-Rad CFX96 Touch and Applied Biosystems™ Quant Studio 5 Real-Time PCR Detection System, , N gene.

Techniques: CRISPR

Journal: Expert Review of Molecular Diagnostics

Article Title: Recent advances in the diagnosis of COVID-19: a bird’s eye view

doi: 10.1080/14737159.2021.1874354

Figure Lengend Snippet: Illustration showing the detection window of SARS-CoV-2 specific viral RNA and antibodies

Article Snippet: 25. , Quick SARS-CoV-2 rRT-PCR Kit (USA) by Zymo Research Corp/R3011/ [ ] , Bio-Rad CFX96 Touch and Applied Biosystems™ Quant Studio 5 Real-Time PCR Detection System, , N gene.

Techniques:

Journal: Expert Review of Molecular Diagnostics

Article Title: Recent advances in the diagnosis of COVID-19: a bird’s eye view

doi: 10.1080/14737159.2021.1874354

Figure Lengend Snippet: List of antigen and antibody-based rapid detection kits approved by FDA

Article Snippet: 25. , Quick SARS-CoV-2 rRT-PCR Kit (USA) by Zymo Research Corp/R3011/ [ ] , Bio-Rad CFX96 Touch and Applied Biosystems™ Quant Studio 5 Real-Time PCR Detection System, , N gene.

Techniques: Surround Optical-fiber Immunoassay

Journal: Expert Review of Molecular Diagnostics

Article Title: Recent advances in the diagnosis of COVID-19: a bird’s eye view

doi: 10.1080/14737159.2021.1874354

Figure Lengend Snippet: Different diagnostic methods and their performance

Article Snippet: 25. , Quick SARS-CoV-2 rRT-PCR Kit (USA) by Zymo Research Corp/R3011/ [ ] , Bio-Rad CFX96 Touch and Applied Biosystems™ Quant Studio 5 Real-Time PCR Detection System, , N gene.

Techniques: Diagnostic Assay, Reverse Transcription Polymerase Chain Reaction, Infection, RT Lamp Assay, Fluorescence, Enzyme-linked Immunosorbent Assay, CRISPR, Negative Control, Computed Tomography, Imaging

Journal: Expert Review of Molecular Diagnostics

Article Title: Recent advances in the diagnosis of COVID-19: a bird’s eye view

doi: 10.1080/14737159.2021.1874354

Figure Lengend Snippet: An overview of the diagnostic methods for SARS-CoV-2

Article Snippet: 25. , Quick SARS-CoV-2 rRT-PCR Kit (USA) by Zymo Research Corp/R3011/ [ ] , Bio-Rad CFX96 Touch and Applied Biosystems™ Quant Studio 5 Real-Time PCR Detection System, , N gene.

Techniques: Diagnostic Assay

Journal: Cell

Article Title: Derivation of Pluripotent Stem Cells with In Vivo Embryonic and Extraembryonic Potency

doi: 10.1016/j.cell.2017.02.005

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Quantitative PCR analysis was conducted using the KAPA SYBR FAST qPCR Kit on a Bio RAD CFX Connect Real-Time System.

Techniques: Recombinant, Knock-Out, Modification, Embryo Culture, Purification, Reporter Assay, SYBR Green Assay, Lysis, Software, High Content Screening

Journal: Pathogens

Article Title: Direct Diagnosis of Echovirus 12 Meningitis Using Metagenomic Next Generation Sequencing

doi: 10.3390/pathogens10050610

Figure Lengend Snippet: Echovirus 12 whole genome sequencing direct diagnosis workflow. The total duration of the handling process is less than 24 h including al steps. ( A ) CSF sampling by lumbar puncture, followed by specific point-of-care (POC) enterovirus (EVs) diagnosis in FilmArray ® CSF direct test (BioFire Diagnostics, Salt Lake City, UT, USA). The viral RNA was extracted and purified following an in-house developed protocol, using QIAamp Viral RNA Mini Kit (Qiagen) and RNA was purified by magnetic DynaBeads (Thermo Fisher, Waltham, MA, USA). The EVs POC diagnostic was confirmed by real-time PCR using LightCycler Multiplex RNA Virus Master kit (Roche Diagnostics ® , Mannheim, Germany). ( B ) The extracted RNA was treated by Turbo DNase (Thermo Fisher) and purified with (Zymo Research) kit. RT-cDNA synthesis reaction was performed in 50 µL-volume using kit TaqMan (Thermo Fisher), followed by double strand synthesis using DNA Polymerase I, Large (Klenow) Fragment (BioLabs). ( C ) The double stranded cDNA sequenced in 150-cycle iSeq Illumina instrument following Nextera NGS library preparation iSeq protocol. Finally, NGS data analysis was performed using CLC Genomics Workbench software version 7.5.0 (Qiagen), and more than 81.68% of Echovirus 12 genome was obtained directly by next-generation sequencing.

Article Snippet: In parallel, total RNA was manually extracted from 200 μL of CSF, following an in-house developed protocol, using QIAamp Viral RNA Mini Kit solutions (Qiagen, Hilden, Germany) for lysing, and washing steps, then total RNA was then purified using RNA specific magnetic Dynabeads (Life technology, Oslo, Norway).

Techniques: Sequencing, Biomarker Discovery, Sampling, Purification, Diagnostic Assay, Real-time Polymerase Chain Reaction, Multiplex Assay, Virus, cDNA Synthesis, Software, Next-Generation Sequencing