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incucyte base analysis software sartorius n a bedtools quinlan hall94  (Sartorius AG)


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    Structured Review

    Sartorius AG incucyte base analysis software sartorius n a bedtools quinlan hall94
    Incucyte Base Analysis Software Sartorius N A Bedtools Quinlan Hall94, supplied by Sartorius AG, used in various techniques. Bioz Stars score: 99/100, based on 16012 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/bedtools+software/Live+Cell+Analysis+Instruments/pm37516102-805-9-13
    Average 99 stars, based on 16012 article reviews
    incucyte base analysis software sartorius n a bedtools quinlan hall94 - by Bioz Stars, 2026-10
    99/100 stars

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    Software:

    Article Title: Multi-level functional genomics reveals molecular and cellular oncogenicity of patient-based 3' untranslated region mutations.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Gibson Assembly Master Mix NEB E2611 Monarch DNA Gel Extraction Kit NEB T1020 Monarch PCR & DNA Cleanup Kit NEB T1030 Phusion High-Fidelity DNA Polymerase NEB M0530 Q5 High Fidelity 2X Master Mix NEB M0492S Q5 Site-Directed Mutagenesis Kit NEB E0554 Q5 High-Fidelity DNA Polymerase NEB M0491 Dual Luciferase Reporter Assay System Promega E1980 DNeasy Blood & Tissue Kit Qiagen 69504 QIAprep Spin Miniprep Kit Qiagen 27104 RNeasy MinElute Cleanup Kit Qiagen 74204 RNeasy Plus Mini Kit Qiagen 74134 Phusion High-Fidelity PCR Master Mix with HF Buffer Thermo Scientific F531S Direct-zol RNA Miniprep Plus Kit Zymo Research ZR2070 DNA Clean and Concentrator Zymo Research 11-302C Deposited data MPRA sequencing data (plasmid, polysome, and IVT) Gene Expression Omnibus GEO: GSE200304 All custom code Zenodo/Github Zenodo: https://doi.org/10.5281/zenodo.8007705 Experimental models: Cell lines HEK293T cells ATCC CRL-3216 PC3 cells ATCC CRL-1435 LNCaP cells ATCC CRL-1740 Oligonucleotides IDT for Illumina Nextera UDI, Set A Illumina 20027213 IDT for Illumina Nextera UDI, Set C Illumina 20042666 ON-TARGETplus Non-targeting Control Pool Dharmacon D-001810-10-05 ON-TARGETplus Human HNRNPD siRNA SMARTpool Dharmacon L-004079-00-0005 ON-TARGETplus Human NCL siRNA Dharmacon L-003854-00-0005 ON-TARGETplus Human ELAVL1 siRNA Dharmacon L-003773-00-0005 ON-TARGETplus Human KHSRP siRNA Dharmacon L-009490-00-0005 ON-TARGETplus Human TIAL1 siRNA Dharmacon L-011405-00-0005 Individual primers for PCR, etc IDT Table S7A eBlocks Gene Fragments (GPRIN3 & IGF1R) IDT Table S7B Recombinant DNA evoAPOBEC1-BE4max cytosine base editor Thuronyi et al.89 Addgene 122611 NG-ABE8e adenine base editor Richter et al.90 Addgene 138491 pFYF1548 EMX1 sgRNA plasmid backbone Fu et al.91 Addgene 47508 pLuc2CP-ARE Younis et al.92 Addgene 62857 pDualLuc Arvind Subramaniam N/A Nanoluciferase exogenous spike-in control This study N/A pIGF1R_sgRNA This study N/A pZWILCH_sgRNA This study N/A pLuc2CP-noARE This study N/A pRL-UBC This study N/A Software and algorithms ImageJ Schneider et al.93 https://ImageJ.nih.gov/ij/ (Continued on next page) Cell Reports 42, 112840, August 29, 2023 19 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER GraphPad Prism GraphPad www.graphpad.com IncuCyte Base Analysis Software Sartorius N/A BEDtools Quinlan & Hall94 https://bedtools.readthedocs.io/en/latest/t Bowtie2 (v2.4.2) Langmead & Salzberg95 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtmlt Picard (v2.25.0) N/A http://broadinstitute.github.io/picard GATK (v4.2.5) Van der Auwera & O’Connor96 https://gatk.broadinstitute.org/hc/en-us XenofiltR Kluin et al.97 https://github.com/NKI-GCF/XenofilteR Mutect2 (v2) Benjamin et al.26 https://gatk.broadinstitute.org/hc/ en-us/articles/360037593851-Mutect2 Strelka (v2.9.2) Kim et al.27 https://github.com/Illumina/strelka MuSE (v2.0) Fan et al.28 https://bioinformatics.mdanderson.org/ public-software/muse/ VarScan2 Koboldt et al.29 https://varscan.sourceforge.net/ ANNOVAR Wang et al.98 https://annovar.openbioinformatics.org/en/latest/ DeconstructSigs Rosenthal et al.99 https://github.com/raerose01/ deconstructSigs GenomicFeatures Lawrence et al.100 https://bioconductor.org/packages/ GenomicFeatures BSgenome.Hsapiens.UCSC.hg38 N/A https://doi.org/10.18129/B9.bioc.BSgenome. .. Hsapiens.UCSC.hg38 edgeR Robinson et al.101 https://bioconductor.org/packages/edgeR ggplot2 Wickham102 https://ggplot2.tidyverse.org/ xtail (v1.1.15) Xiao et al.103 https://github.com/xryanglab/xtail nlstools Baty et al.104 https://github.com/aursiber/nlstools STAR (v2.7.3a) Dobin et al.105 https://github.com/alexdobin/STAR HTSeq (0.11.0) Anders et al.106 https://htseq.readthedocs.io/en/master/ DESeq2 Love et al.107 https://github.com/mikelove/DESeq2 Enrichr Chen et al.108 https://maayanlab.cloud/Enrichr/ survminer N/A rpkgs.datanovia.com/survminer/ GenomicScores Puigdevall and Castelo109 https://github.com/rcastelo/GenomicScores ViennaRNA Lorenz et al.80 https://www.tbi.univie.ac.at/RNA/ EditR Kluesner et al.110 http://baseeditr.com/ Pyclone (v0.13.1) Roth et al.111 https://github.com/Roth-Lab/pyclone Sequenza (v3.0.0) Favero et al.112 https://bitbucket.org/sequenzatools/ sequenza/src/master/ FishHook (v0.1) Imielinski et al.43 https://github.com/mskilab/fishHook/tree/master Article ll OPEN ACCESS



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