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algorithms prism graphpad software  (Biognosys)

 
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    Biognosys algorithms prism graphpad software
    Algorithms Prism Graphpad Software, supplied by Biognosys, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/software+graphpad/algorithms+graphpad+prism+software/pm41747732-295-59-89
    Average 86 stars, based on 1 article reviews
    algorithms prism graphpad software - by Bioz Stars, 2026-10
    86/100 stars

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    Software:

    Article Title: Functional nutrient-genetic profiling reveals biotin and FBXW7 are essential to bypass glutamine addiction.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data 13 C- and 15 N-glutamine isotopic profiling in K562; 13 C-pyruvate isotopic profiling in primary CD8 + T cells This study MTBLS13799 13 C-pyruvate isotopic profiling in K562 This study 14002048 Multiple pathway targeted analysis of polar metabolites This study 14002048 Mass spectrometry data This study PXD057389 Spheroid imaging data This study https://www.doi.org/10.17632/328g7zyt9d.1 K562 RNAseq Slavoff et al. 81 GSE34740 Transcription factor ChIP-seq in K562 ENCODE 68 MYC(ENCFF801QJW), MNT(ENCFF611RGV), SIN3A(ENCFF085NLG) H3K27ac ChIP-seq in K562 ENCODE 68 ENCFF381NDD Experimental models: Cell lines Human: K562 American Type Culture Collection (ATCC) Cat# CCL-243; RRID: CVCL_0004 Human: HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Human: HeLa ATCC Cat# CCL-2; RRID: CVCL_0030 Human: MCF-7 ATCC Cat# HTB-22; RRID: CVCL_0031 Human: SW480 ATCC Cat# CCL-228; RRID: CVCL_0546 Human: UACC-257 Frederick Cancer Division of Cancer Treatment and Diagnostic (DCTD) RRID: CVCL_1779 Human: U-2 OS ATCC Cat# HTB-96; RRID: CVCL_0042 Human: A375 ATCC Cat# CRL-1619; RRID: CVCL_0132 Mouse: MC38 Sigma-Aldrich Cat# SCC172; RRID: CVCL_B288 Mouse: B16-F10 ATCC Cat# CRL-6475; RRID: CVCL_0159 Mouse: MycER mouse embryonic fibroblast Wise et al. 9 ; Linder et al. 19 N/A Oligonucleotides sgRNAs, see Table S9 Integrated DNA Technologies N/A ChIP primers, see Table S9 Integrated DNA Technologies N/A Random hexamers ThermoFisher Cat# N8080127 TaqMan Gene Expression Assay, human PC, FAM-MGB Life Technologies Cat# Hs01085875_g1 Taqman Gene Expression Assay, human TBP, VIC-MGB Life Technologies Cat# Hs00427620_m1 Recombinant DNA pLX304-GFP-V5 Kim et al. 82 Addgene, Cat# 193687; RRID: Addgene_193687 pLX304-PC Wiemann et al. 83 DNAsu, Cat# HsCD00436386 pWPI-Neo-GFP-3xFLAG Jourdain et al. 84 Addgene, Cat# 201639; RRID: Addgene_201639 pWPI-SLC7A11-HA Jourdain et al. 84 Addgene, Cat# 201643; RRID: Addgene_201643 pMXS-SLC1A3 Birsoy et al. 30 Addgene, Cat# 72873; RRID: Addgene_72873 pLVX-TetOne-Puro-GFP-3xFLAG This study N/A pLVX-TetOne-Puro-LbNOX Titov et al. 31 and Choe et al. 85 Addgene, Cat# 234984; RRID: Addgene_234984 pTwist-Lenti-CMV-BSD-GFP-3xFLAG This study Twist Bioscience pTwist-Lenti-CMV-BSD-PC-WT This study Twist Bioscience pTwist-Lenti-CMV-BSD-PC-K1144R This study Twist Bioscience pTwist-Lenti-CMV-Puro-FBXW7-WT This study Twist Bioscience pTwist-Lenti-CMV-Puro-FBXW7-R465C This study Twist Bioscience (Continued on next page) Molecular Cell 86, 901–916.e1–e10, March 5, 2026 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER pTwist-Lenti-CMV-Puro-FBXW7-R505C This study Twist Bioscience pTwist-Lenti-CMV-Puro-FBXW7-R479Q This study Twist Bioscience psPAX2 Didier Trono Addgene, Cat# 12260; RRID: Addgene_12260 pMD2.G Didier Trono Addgene, Cat# 12259; RRID: Addgene_12259 lentiCRISPR v2 Sanjana et al. 86 Addgene, Cat# 52961; RRID: Addgene_52961 Human sgRNA library Brunello (lentiCRISPR v2) Sanson et al. 87 Addgene, Cat# 73179; RRID: Addgene_73179 Software and algorithms Prism GraphPad Software https://www.graphpad.com/ Fiji Schindelin et al. 88 https://imagej.net/software/fiji/ IGV Robinson et al. 89 https://igv.org/ GSEA Subramanian et al. 90 https://www.gsea-msigdb.org/gsea/index.jsp MetaboAnalyst Pang et al. 29 https://www.metaboanalyst.ca/ Spectronaut Biognosys Schlieren https://biognosys.com/software/spectronaut/ IDPicker algorithm Ma et al. 91 https://proteowizard.sourceforge.io/idpicker/ MaxLFQ algorithm Cox et al. 92 https://www.maxquant.org/ Perseus Tyanova et al. 93 https://maxquant.net/perseus/ MassHunter Quantitative Analysis Agilent Technologies https://www.agilent.com/en/product/ software-informatics/massspectrometry-software ProFinder Agilent Technologies https://www.agilent.com/en/product/ software-informatics/massspectrometry-software/dataanalysis/mass-profilerprofessional-software R R Core Team 94 http://cran.r-project.org/ LOWESS/Spline normalization algorithm Tsugawa et al. 95 http://prime.psc.riken.jp Xcalibur ThermoFisher https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/ liquid-chromatography-massspectrometry-lc-ms/lc-ms-software/ lc-ms-data-acquisition-software/ xcalibur-data-acquisitioninterpretation-software.html Compound Discoverer ThermoFisher https://www.thermofisher.com/ch/ en/home/industrial/mass-spectrometry/ liquid-chromatography-massspectrometry-lc-ms/lc-ms-software/ multi-omics-data-analysis/compounddiscoverer-software.html?cid= E.25CMD.CD103.25418.01 Skyline University of Washington https://skyline.ms/home/software/ Skyline/project-begin.view Other U-bottom NunclonTM SpheraTM 96-Well plates ThermoFisher Cat# 174925 NuncTM MicroWellTM 96-Well plates Nunc Cat# 137101 8-16% NovexTM WedgeWellTM Tris-Glycine gels ThermoFisher Cat# XP08160BOX Dynabeads Protein G ThermoFisher Cat# 10007D Dynabeads Protein A ThermoFisher Cat# 10001D e4 Molecular Cell 86, 901–916.e1–e10, March 5, 2026 .. K562 (ATCC, CCL-243), HEK293T (ATCC, CRL-3216, referred to as 293T), HeLa (ATCC, CCL-2), MCF7 (ATCC, HTB-22), SW480 (ATCC, CCL-228), UACC-257 (DCTD, CVCL_1779), U-2 OS (ATCC, HTB-96), A375 (CRL-1619), MC38 (CRL-2640) and B16-F10 (CRL-6475) were maintained under standard cell culture conditions in DMEM containing 25 mM glucose, 1 mM sodium pyruvate, 2 mM glutamine, and supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin/streptomycin.

    Targeted Proteomics:

    Article Title: Functional nutrient-genetic profiling reveals biotin and FBXW7 are essential to bypass glutamine addiction.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data 13 C- and 15 N-glutamine isotopic profiling in K562; 13 C-pyruvate isotopic profiling in primary CD8 + T cells This study MTBLS13799 13 C-pyruvate isotopic profiling in K562 This study 14002048 Multiple pathway targeted analysis of polar metabolites This study 14002048 Mass spectrometry data This study PXD057389 Spheroid imaging data This study https://www.doi.org/10.17632/328g7zyt9d.1 K562 RNAseq Slavoff et al. 81 GSE34740 Transcription factor ChIP-seq in K562 ENCODE 68 MYC(ENCFF801QJW), MNT(ENCFF611RGV), SIN3A(ENCFF085NLG) H3K27ac ChIP-seq in K562 ENCODE 68 ENCFF381NDD Experimental models: Cell lines Human: K562 American Type Culture Collection (ATCC) Cat# CCL-243; RRID: CVCL_0004 Human: HEK293T ATCC Cat# CRL-3216; RRID: CVCL_0063 Human: HeLa ATCC Cat# CCL-2; RRID: CVCL_0030 Human: MCF-7 ATCC Cat# HTB-22; RRID: CVCL_0031 Human: SW480 ATCC Cat# CCL-228; RRID: CVCL_0546 Human: UACC-257 Frederick Cancer Division of Cancer Treatment and Diagnostic (DCTD) RRID: CVCL_1779 Human: U-2 OS ATCC Cat# HTB-96; RRID: CVCL_0042 Human: A375 ATCC Cat# CRL-1619; RRID: CVCL_0132 Mouse: MC38 Sigma-Aldrich Cat# SCC172; RRID: CVCL_B288 Mouse: B16-F10 ATCC Cat# CRL-6475; RRID: CVCL_0159 Mouse: MycER mouse embryonic fibroblast Wise et al. 9 ; Linder et al. 19 N/A Oligonucleotides sgRNAs, see Table S9 Integrated DNA Technologies N/A ChIP primers, see Table S9 Integrated DNA Technologies N/A Random hexamers ThermoFisher Cat# N8080127 TaqMan Gene Expression Assay, human PC, FAM-MGB Life Technologies Cat# Hs01085875_g1 Taqman Gene Expression Assay, human TBP, VIC-MGB Life Technologies Cat# Hs00427620_m1 Recombinant DNA pLX304-GFP-V5 Kim et al. 82 Addgene, Cat# 193687; RRID: Addgene_193687 pLX304-PC Wiemann et al. 83 DNAsu, Cat# HsCD00436386 pWPI-Neo-GFP-3xFLAG Jourdain et al. 84 Addgene, Cat# 201639; RRID: Addgene_201639 pWPI-SLC7A11-HA Jourdain et al. 84 Addgene, Cat# 201643; RRID: Addgene_201643 pMXS-SLC1A3 Birsoy et al. 30 Addgene, Cat# 72873; RRID: Addgene_72873 pLVX-TetOne-Puro-GFP-3xFLAG This study N/A pLVX-TetOne-Puro-LbNOX Titov et al. 31 and Choe et al. 85 Addgene, Cat# 234984; RRID: Addgene_234984 pTwist-Lenti-CMV-BSD-GFP-3xFLAG This study Twist Bioscience pTwist-Lenti-CMV-BSD-PC-WT This study Twist Bioscience pTwist-Lenti-CMV-BSD-PC-K1144R This study Twist Bioscience pTwist-Lenti-CMV-Puro-FBXW7-WT This study Twist Bioscience pTwist-Lenti-CMV-Puro-FBXW7-R465C This study Twist Bioscience (Continued on next page) Molecular Cell 86, 901–916.e1–e10, March 5, 2026 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER pTwist-Lenti-CMV-Puro-FBXW7-R505C This study Twist Bioscience pTwist-Lenti-CMV-Puro-FBXW7-R479Q This study Twist Bioscience psPAX2 Didier Trono Addgene, Cat# 12260; RRID: Addgene_12260 pMD2.G Didier Trono Addgene, Cat# 12259; RRID: Addgene_12259 lentiCRISPR v2 Sanjana et al. 86 Addgene, Cat# 52961; RRID: Addgene_52961 Human sgRNA library Brunello (lentiCRISPR v2) Sanson et al. 87 Addgene, Cat# 73179; RRID: Addgene_73179 Software and algorithms Prism GraphPad Software https://www.graphpad.com/ Fiji Schindelin et al. 88 https://imagej.net/software/fiji/ IGV Robinson et al. 89 https://igv.org/ GSEA Subramanian et al. 90 https://www.gsea-msigdb.org/gsea/index.jsp MetaboAnalyst Pang et al. 29 https://www.metaboanalyst.ca/ Spectronaut Biognosys Schlieren https://biognosys.com/software/spectronaut/ IDPicker algorithm Ma et al. 91 https://proteowizard.sourceforge.io/idpicker/ MaxLFQ algorithm Cox et al. 92 https://www.maxquant.org/ Perseus Tyanova et al. 93 https://maxquant.net/perseus/ MassHunter Quantitative Analysis Agilent Technologies https://www.agilent.com/en/product/ software-informatics/massspectrometry-software ProFinder Agilent Technologies https://www.agilent.com/en/product/ software-informatics/massspectrometry-software/dataanalysis/mass-profilerprofessional-software R R Core Team 94 http://cran.r-project.org/ LOWESS/Spline normalization algorithm Tsugawa et al. 95 http://prime.psc.riken.jp Xcalibur ThermoFisher https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/ liquid-chromatography-massspectrometry-lc-ms/lc-ms-software/ lc-ms-data-acquisition-software/ xcalibur-data-acquisitioninterpretation-software.html Compound Discoverer ThermoFisher https://www.thermofisher.com/ch/ en/home/industrial/mass-spectrometry/ liquid-chromatography-massspectrometry-lc-ms/lc-ms-software/ multi-omics-data-analysis/compounddiscoverer-software.html?cid= E.25CMD.CD103.25418.01 Skyline University of Washington https://skyline.ms/home/software/ Skyline/project-begin.view Other U-bottom NunclonTM SpheraTM 96-Well plates ThermoFisher Cat# 174925 NuncTM MicroWellTM 96-Well plates Nunc Cat# 137101 8-16% NovexTM WedgeWellTM Tris-Glycine gels ThermoFisher Cat# XP08160BOX Dynabeads Protein G ThermoFisher Cat# 10007D Dynabeads Protein A ThermoFisher Cat# 10001D e4 Molecular Cell 86, 901–916.e1–e10, March 5, 2026 .. K562 (ATCC, CCL-243), HEK293T (ATCC, CRL-3216, referred to as 293T), HeLa (ATCC, CCL-2), MCF7 (ATCC, HTB-22), SW480 (ATCC, CCL-228), UACC-257 (DCTD, CVCL_1779), U-2 OS (ATCC, HTB-96), A375 (CRL-1619), MC38 (CRL-2640) and B16-F10 (CRL-6475) were maintained under standard cell culture conditions in DMEM containing 25 mM glucose, 1 mM sodium pyruvate, 2 mM glutamine, and supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin/streptomycin.



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