Construct:Article Title: Methods and compositions for treating RNA viral infections
Article Snippet: .. The lentivirus was created by co-transfection of HEK293T cells with pBOB-hACE2 construct and lentiviral packaging plasmids pMDL, pREV, and pVSV-G (Addgene) using Lipofectamine 2000 (Thermo Fisher Scientific, 11668019). ..
Transduction:Article Title: The lipid transfer protein STARD7 controls intestinal tumor development in a context-dependent manner.
Article Snippet: .. Lentiviral vector production and cell transduction Transfection mixture was prepared in 800 μL OptiMEM (Gibco) by adding following plasmids: 12 μg of psPAX2 (AddGene #12260), 5 μg of pVSV-G (AddGene #138479) and 12 μg of expression vector carrying shRNA sequence, in the presence of 80 μL of TransIT-LT1 Transfection Reagent (Mirus, Mir2360). .. Expression vectors were: pLVshCtrl (Sigma, SHC002), pLVshSTARD7#2 (Sigma, TRCN000028081), pLVshSTARD7#4 (Sigma, TRCN0000155648).
Transfection:Article Title: The lipid transfer protein STARD7 controls intestinal tumor development in a context-dependent manner.
Article Snippet: .. Lentiviral vector production and cell transduction Transfection mixture was prepared in 800 μL OptiMEM (Gibco) by adding following plasmids: 12 μg of psPAX2 (AddGene #12260), 5 μg of pVSV-G (AddGene #138479) and 12 μg of expression vector carrying shRNA sequence, in the presence of 80 μL of TransIT-LT1 Transfection Reagent (Mirus, Mir2360). .. Expression vectors were: pLVshCtrl (Sigma, SHC002), pLVshSTARD7#2 (Sigma, TRCN000028081), pLVshSTARD7#4 (Sigma, TRCN0000155648).
Article Title: SMN deficiency-induced alternative splicing dysregulation in cardiac defects.
Article Snippet: This is a PDF of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability.. This version will undergo additional copyediting, typesetting and review before it is published in its final form.. As such, this version is no longer the Accepted Manuscript, but it is not yet the definitive Version of Record; we are providing this early version to give early visibility of the article.
Article Title: A Functionally Conserved Enhancer is Critical for PGC1A Expression and Thermogenesis in Brown Fat.
Article Snippet: .. A total of 95 μg of plasmid DNA, consisting of the transfer plasmid pLV-hU6-sgRNA-hUbC-dCas9-KRAB-T2a-GFP (Addgene #71237), the packaging plasmid psPAX2 (Addgene #12260), and the envelope plasmid pVSV-G (Addgene #138479), was mixed at a weight ratio of 4:3:1 and introduced into the cells using a Calcium Phosphate Transfection Kit (Beyotime, Shanghai, China). .. The culture medium was replaced 8 h posttransfection, and viral supernatants were collected at 24, 48, and 72 h. The pooled supernatants were concentrated using Microsep Advance Centrifugal Devices with Omega Membrane 100K (PALL).
Article Title: Pulmonary surfactant protein D reduces lung cancer progression associated with decreased IL-4/STAT6 signaling.
Article Snippet: The vectors were sequence verified by Sanger sequencing (Eurofins Genomics). .. HEK293T cells were transfected with packaging plasmids pVSVG (Addgene plasmid # 138479 ; http://n2t.net/addgene:138479 ; RRID:Addgene_138479) AR TI CL E IN P RE SS was a gift from Akitsu Hotta 51. pRSV-Rev (Addgene plasmid # 12253 ; http://n2t.net/addgene:12253 ; RRID:Addgene_12253) and pMDL g/p RRE (Addgene plasmid # 12251 ; http://n2t.net/addgene:12251 ; RRID:Addgene_12251) was a gift from Didier Trone 52. ..
Expressing:Article Title: The lipid transfer protein STARD7 controls intestinal tumor development in a context-dependent manner.
Article Snippet: .. Lentiviral vector production and cell transduction Transfection mixture was prepared in 800 μL OptiMEM (Gibco) by adding following plasmids: 12 μg of psPAX2 (AddGene #12260), 5 μg of pVSV-G (AddGene #138479) and 12 μg of expression vector carrying shRNA sequence, in the presence of 80 μL of TransIT-LT1 Transfection Reagent (Mirus, Mir2360). .. Expression vectors were: pLVshCtrl (Sigma, SHC002), pLVshSTARD7#2 (Sigma, TRCN000028081), pLVshSTARD7#4 (Sigma, TRCN0000155648).
shRNA:Article Title: The lipid transfer protein STARD7 controls intestinal tumor development in a context-dependent manner.
Article Snippet: .. Lentiviral vector production and cell transduction Transfection mixture was prepared in 800 μL OptiMEM (Gibco) by adding following plasmids: 12 μg of psPAX2 (AddGene #12260), 5 μg of pVSV-G (AddGene #138479) and 12 μg of expression vector carrying shRNA sequence, in the presence of 80 μL of TransIT-LT1 Transfection Reagent (Mirus, Mir2360). .. Expression vectors were: pLVshCtrl (Sigma, SHC002), pLVshSTARD7#2 (Sigma, TRCN000028081), pLVshSTARD7#4 (Sigma, TRCN0000155648).
Sequencing:Article Title: The lipid transfer protein STARD7 controls intestinal tumor development in a context-dependent manner.
Article Snippet: .. Lentiviral vector production and cell transduction Transfection mixture was prepared in 800 μL OptiMEM (Gibco) by adding following plasmids: 12 μg of psPAX2 (AddGene #12260), 5 μg of pVSV-G (AddGene #138479) and 12 μg of expression vector carrying shRNA sequence, in the presence of 80 μL of TransIT-LT1 Transfection Reagent (Mirus, Mir2360). .. Expression vectors were: pLVshCtrl (Sigma, SHC002), pLVshSTARD7#2 (Sigma, TRCN000028081), pLVshSTARD7#4 (Sigma, TRCN0000155648).
Article Title: Targeting PGAM5-driven mitochondrial integrated stress response slows ALS progression across subtypes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides See Table S3 for the sequence information of qPCR primers, shRNAs, siRNAs and sgRNAs This study N/A Recombinant DNA pMSCV-F-del-Casp9-IRES-GFP Straathof et al. 98 Addgene plasmid# 15567 rtTA-N144 Richner et al. 99 Addgene plasmid# 66810 pXG237 Guo et al. 40 Addgene plasmid# 141281 pRK5-HA-Ubiquitin-WT Lim et al. 100 Addgene plasmid# 17608 pMDLg/pRRE Dull et al. 101 Addgene plasmid# 12251 pRSV-Rev Dull et al. 101 Addgene plasmid# 12253 psPAX2 A gift from Didier Trono Addgene plasmid# 12260 pMD2.G A gift from Didier Trono Addgene plasmid# 12259 pVSV-G Dull et al. 101 Addgene plasmid# 138479 pLKO.1 Moffat et al. 102 Addgene plasmid# 10878 pHAGE-CMV-MCS-PGK-Puro Clontech Laboratories N/A pGEX-6P-1-GST Cytiva Cat# 28954648 pET-28a(+)-HIS MERCK Cat# 69864 pCMV-Myc Takara Bio Cat# 635689 Myc-VCP and mutants This study N/A uORFs-iCasp9-HA This study N/A pHAGE-PGAM5-3xFlag and mutants This study N/A GST-PGAM5 and mutants This study N/A His-OMA1 This study N/A His-PO1 This study N/A HA-OMA1 and mutants This study N/A pHAGE-DELE1-3xFlag This study N/A Software and algorithms Maestro Schrö dinger https://www.schrodinger.com/platform/ products/maestro/ GraphPad Prism GraphPad https://www.graphpad.com/ scientificsoftware/prism/ GSEA Broad Institute http://software.broadinstitute.org/gsea/ login.jsp ImageJ ImageJ https://imagej.nih.gov/ij/ ZEN 2.3 (blue edition) Carl Zeiss https://www.zeiss.com/microscopy/en/ products/software/zeiss-zen.html R version 4.4.0 The R Foundation https://www.r-project.org/ Neuron 114, 1–19.e1–e14, June 17, 2026 e6 ..
Purification:Article Title: SMN deficiency-induced alternative splicing dysregulation in cardiac defects.
Article Snippet: This is a PDF of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability.. This version will undergo additional copyediting, typesetting and review before it is published in its final form.. As such, this version is no longer the Accepted Manuscript, but it is not yet the definitive Version of Record; we are providing this early version to give early visibility of the article.
Plasmid Preparation:Article Title: SMN deficiency-induced alternative splicing dysregulation in cardiac defects.
Article Snippet: This is a PDF of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability.. This version will undergo additional copyediting, typesetting and review before it is published in its final form.. As such, this version is no longer the Accepted Manuscript, but it is not yet the definitive Version of Record; we are providing this early version to give early visibility of the article.
Article Title: Targeting PGAM5-driven mitochondrial integrated stress response slows ALS progression across subtypes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides See Table S3 for the sequence information of qPCR primers, shRNAs, siRNAs and sgRNAs This study N/A Recombinant DNA pMSCV-F-del-Casp9-IRES-GFP Straathof et al. 98 Addgene plasmid# 15567 rtTA-N144 Richner et al. 99 Addgene plasmid# 66810 pXG237 Guo et al. 40 Addgene plasmid# 141281 pRK5-HA-Ubiquitin-WT Lim et al. 100 Addgene plasmid# 17608 pMDLg/pRRE Dull et al. 101 Addgene plasmid# 12251 pRSV-Rev Dull et al. 101 Addgene plasmid# 12253 psPAX2 A gift from Didier Trono Addgene plasmid# 12260 pMD2.G A gift from Didier Trono Addgene plasmid# 12259 pVSV-G Dull et al. 101 Addgene plasmid# 138479 pLKO.1 Moffat et al. 102 Addgene plasmid# 10878 pHAGE-CMV-MCS-PGK-Puro Clontech Laboratories N/A pGEX-6P-1-GST Cytiva Cat# 28954648 pET-28a(+)-HIS MERCK Cat# 69864 pCMV-Myc Takara Bio Cat# 635689 Myc-VCP and mutants This study N/A uORFs-iCasp9-HA This study N/A pHAGE-PGAM5-3xFlag and mutants This study N/A GST-PGAM5 and mutants This study N/A His-OMA1 This study N/A His-PO1 This study N/A HA-OMA1 and mutants This study N/A pHAGE-DELE1-3xFlag This study N/A Software and algorithms Maestro Schrö dinger https://www.schrodinger.com/platform/ products/maestro/ GraphPad Prism GraphPad https://www.graphpad.com/ scientificsoftware/prism/ GSEA Broad Institute http://software.broadinstitute.org/gsea/ login.jsp ImageJ ImageJ https://imagej.nih.gov/ij/ ZEN 2.3 (blue edition) Carl Zeiss https://www.zeiss.com/microscopy/en/ products/software/zeiss-zen.html R version 4.4.0 The R Foundation https://www.r-project.org/ Neuron 114, 1–19.e1–e14, June 17, 2026 e6 ..
Article Title: A Functionally Conserved Enhancer is Critical for PGC1A Expression and Thermogenesis in Brown Fat.
Article Snippet: .. A total of 95 μg of plasmid DNA, consisting of the transfer plasmid pLV-hU6-sgRNA-hUbC-dCas9-KRAB-T2a-GFP (Addgene #71237), the packaging plasmid psPAX2 (Addgene #12260), and the envelope plasmid pVSV-G (Addgene #138479), was mixed at a weight ratio of 4:3:1 and introduced into the cells using a Calcium Phosphate Transfection Kit (Beyotime, Shanghai, China). .. The culture medium was replaced 8 h posttransfection, and viral supernatants were collected at 24, 48, and 72 h. The pooled supernatants were concentrated using Microsep Advance Centrifugal Devices with Omega Membrane 100K (PALL).
Article Title: Pulmonary surfactant protein D reduces lung cancer progression associated with decreased IL-4/STAT6 signaling.
Article Snippet: The vectors were sequence verified by Sanger sequencing (Eurofins Genomics). .. HEK293T cells were transfected with packaging plasmids pVSVG (Addgene plasmid # 138479 ; http://n2t.net/addgene:138479 ; RRID:Addgene_138479) AR TI CL E IN P RE SS was a gift from Akitsu Hotta 51. pRSV-Rev (Addgene plasmid # 12253 ; http://n2t.net/addgene:12253 ; RRID:Addgene_12253) and pMDL g/p RRE (Addgene plasmid # 12251 ; http://n2t.net/addgene:12251 ; RRID:Addgene_12251) was a gift from Didier Trone 52. ..
Real-time Polymerase Chain Reaction:Article Title: Targeting PGAM5-driven mitochondrial integrated stress response slows ALS progression across subtypes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides See Table S3 for the sequence information of qPCR primers, shRNAs, siRNAs and sgRNAs This study N/A Recombinant DNA pMSCV-F-del-Casp9-IRES-GFP Straathof et al. 98 Addgene plasmid# 15567 rtTA-N144 Richner et al. 99 Addgene plasmid# 66810 pXG237 Guo et al. 40 Addgene plasmid# 141281 pRK5-HA-Ubiquitin-WT Lim et al. 100 Addgene plasmid# 17608 pMDLg/pRRE Dull et al. 101 Addgene plasmid# 12251 pRSV-Rev Dull et al. 101 Addgene plasmid# 12253 psPAX2 A gift from Didier Trono Addgene plasmid# 12260 pMD2.G A gift from Didier Trono Addgene plasmid# 12259 pVSV-G Dull et al. 101 Addgene plasmid# 138479 pLKO.1 Moffat et al. 102 Addgene plasmid# 10878 pHAGE-CMV-MCS-PGK-Puro Clontech Laboratories N/A pGEX-6P-1-GST Cytiva Cat# 28954648 pET-28a(+)-HIS MERCK Cat# 69864 pCMV-Myc Takara Bio Cat# 635689 Myc-VCP and mutants This study N/A uORFs-iCasp9-HA This study N/A pHAGE-PGAM5-3xFlag and mutants This study N/A GST-PGAM5 and mutants This study N/A His-OMA1 This study N/A His-PO1 This study N/A HA-OMA1 and mutants This study N/A pHAGE-DELE1-3xFlag This study N/A Software and algorithms Maestro Schrö dinger https://www.schrodinger.com/platform/ products/maestro/ GraphPad Prism GraphPad https://www.graphpad.com/ scientificsoftware/prism/ GSEA Broad Institute http://software.broadinstitute.org/gsea/ login.jsp ImageJ ImageJ https://imagej.nih.gov/ij/ ZEN 2.3 (blue edition) Carl Zeiss https://www.zeiss.com/microscopy/en/ products/software/zeiss-zen.html R version 4.4.0 The R Foundation https://www.r-project.org/ Neuron 114, 1–19.e1–e14, June 17, 2026 e6 ..
Recombinant:Article Title: Targeting PGAM5-driven mitochondrial integrated stress response slows ALS progression across subtypes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides See Table S3 for the sequence information of qPCR primers, shRNAs, siRNAs and sgRNAs This study N/A Recombinant DNA pMSCV-F-del-Casp9-IRES-GFP Straathof et al. 98 Addgene plasmid# 15567 rtTA-N144 Richner et al. 99 Addgene plasmid# 66810 pXG237 Guo et al. 40 Addgene plasmid# 141281 pRK5-HA-Ubiquitin-WT Lim et al. 100 Addgene plasmid# 17608 pMDLg/pRRE Dull et al. 101 Addgene plasmid# 12251 pRSV-Rev Dull et al. 101 Addgene plasmid# 12253 psPAX2 A gift from Didier Trono Addgene plasmid# 12260 pMD2.G A gift from Didier Trono Addgene plasmid# 12259 pVSV-G Dull et al. 101 Addgene plasmid# 138479 pLKO.1 Moffat et al. 102 Addgene plasmid# 10878 pHAGE-CMV-MCS-PGK-Puro Clontech Laboratories N/A pGEX-6P-1-GST Cytiva Cat# 28954648 pET-28a(+)-HIS MERCK Cat# 69864 pCMV-Myc Takara Bio Cat# 635689 Myc-VCP and mutants This study N/A uORFs-iCasp9-HA This study N/A pHAGE-PGAM5-3xFlag and mutants This study N/A GST-PGAM5 and mutants This study N/A His-OMA1 This study N/A His-PO1 This study N/A HA-OMA1 and mutants This study N/A pHAGE-DELE1-3xFlag This study N/A Software and algorithms Maestro Schrö dinger https://www.schrodinger.com/platform/ products/maestro/ GraphPad Prism GraphPad https://www.graphpad.com/ scientificsoftware/prism/ GSEA Broad Institute http://software.broadinstitute.org/gsea/ login.jsp ImageJ ImageJ https://imagej.nih.gov/ij/ ZEN 2.3 (blue edition) Carl Zeiss https://www.zeiss.com/microscopy/en/ products/software/zeiss-zen.html R version 4.4.0 The R Foundation https://www.r-project.org/ Neuron 114, 1–19.e1–e14, June 17, 2026 e6 ..
Software:Article Title: Targeting PGAM5-driven mitochondrial integrated stress response slows ALS progression across subtypes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides See Table S3 for the sequence information of qPCR primers, shRNAs, siRNAs and sgRNAs This study N/A Recombinant DNA pMSCV-F-del-Casp9-IRES-GFP Straathof et al. 98 Addgene plasmid# 15567 rtTA-N144 Richner et al. 99 Addgene plasmid# 66810 pXG237 Guo et al. 40 Addgene plasmid# 141281 pRK5-HA-Ubiquitin-WT Lim et al. 100 Addgene plasmid# 17608 pMDLg/pRRE Dull et al. 101 Addgene plasmid# 12251 pRSV-Rev Dull et al. 101 Addgene plasmid# 12253 psPAX2 A gift from Didier Trono Addgene plasmid# 12260 pMD2.G A gift from Didier Trono Addgene plasmid# 12259 pVSV-G Dull et al. 101 Addgene plasmid# 138479 pLKO.1 Moffat et al. 102 Addgene plasmid# 10878 pHAGE-CMV-MCS-PGK-Puro Clontech Laboratories N/A pGEX-6P-1-GST Cytiva Cat# 28954648 pET-28a(+)-HIS MERCK Cat# 69864 pCMV-Myc Takara Bio Cat# 635689 Myc-VCP and mutants This study N/A uORFs-iCasp9-HA This study N/A pHAGE-PGAM5-3xFlag and mutants This study N/A GST-PGAM5 and mutants This study N/A His-OMA1 This study N/A His-PO1 This study N/A HA-OMA1 and mutants This study N/A pHAGE-DELE1-3xFlag This study N/A Software and algorithms Maestro Schrö dinger https://www.schrodinger.com/platform/ products/maestro/ GraphPad Prism GraphPad https://www.graphpad.com/ scientificsoftware/prism/ GSEA Broad Institute http://software.broadinstitute.org/gsea/ login.jsp ImageJ ImageJ https://imagej.nih.gov/ij/ ZEN 2.3 (blue edition) Carl Zeiss https://www.zeiss.com/microscopy/en/ products/software/zeiss-zen.html R version 4.4.0 The R Foundation https://www.r-project.org/ Neuron 114, 1–19.e1–e14, June 17, 2026 e6 ..
Article Title: Herpes simplex virus 1 fluidizes the nucleus, enabling condensate formation.
Article Snippet: .. REAGENT SOURCE IDENTIFIER pUBC-SV40NLS-popz3h-QtE-GSTSapphire Liam Holt (NYU Langone Health), Addgene # 250610 pLH2259 pUBC-SV40NLS-HoTag3Shunzhi12nm-Sapphire Liam Holt (NYU Langone Health), Addgene #250617 pLH2899 pLVX-TetOn-puro-ICP4 Liam Holt (NYU Langone Health), Addgene #250611 pLH2488 pVSV-G Addgene #138479 pLH2496 gag/pol Addgene #14887 pLH2497 pBABE-puro-Halo-H2A Eli Rothenberg (NYU Langone Health) pLH2498 pLVX-TetOn-puro Meike Dittman (NYU Langone Health) pLH2537 pLVX-TetOn-puro-ICP4-ΔNTA Liam Holt (NYU Langone Health), Addgene #250612 pLH2631 pLVX-TetOne-puro-ICP4-ΔCTA Liam Holt (NYU Langone Health), Addgene #250613 pLH2632 pLVX-TetOn-puro-ICP4-mDBD-RR/LL Liam Holt (NYU Langone Health), Addgene #250614 pLH2658 pLVX-TetOn-puro-ICP4-mDBD-KG/NC Liam Holt (NYU Langone Health), Addgene #250615 pLH2659 p503 jt74 RMCE miRFP670-Halo-HOTag3 Huaiying Zhang (Carnegie Mellon University) pLH2712 p403 jt61 RMCE mScarlet-eDHFR-Mad1 Huaiying Zhang (Carnegie Mellon University) pLH2714 pLVX-TetOn-puro-ICP8 Liam Holt (NYU Langone Health), Addgene #250616 pLH2733 Software and Algorithms Python Open source https://www.python.org/ downloads/release/python-3107/ FIJI (FIJI is just ImageJ) Schindelin et al. 99 https://imagej.net/software/fiji/ MOSAIC for ImageJ Shivanandan et al. 100 https://github.com/mosaic-group/ MosaicSuite foci-counting Tinevez et al. https://github.com/liamholtlab/ foci_counting GEMSpa Keegan et al. 101 https://github.com/liamholtlab/ napari-gemspa (napari plugin), https:// github.com/liamholtlab/GEMspa (stand alone) Cellpose Stringer et al. 102 https://cellpose.readthedocs.io/en/latest/# TrackMate Tinevez et al. 103 https://github.com/trackmate-sc/ TrackMate Nikon Elements Nikon Instruments (2017) https://www.nikoninstruments.com/ Products/Software e3 Molecular Cell 86, 817–833.e1–e7, March 5, 2026 ..
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