Recombinant:Article Title: A TAZ-AXL-ABL2 feed-forward signaling axis promotes lung adenocarcinoma brain metastasis
Article Snippet: Read counts from aligned output files were determined with the Htseq-count tool using reference GTF files obtained from Ensembl. .. Recombinant DNA & Plasmids pLKO-puro Non-Target shRNA Control Sigma Mission TRC1 SHC016-1EA pLKO-puro shAXL 1040 Sigma Mission TRC1 TRCN0000001040 pLKO-puro shTAZ 70 Sigma Mission TRC1 TRCN0000019470 pLKO-puro shTAZ 71 Sigma Mission TRC1 TRCN0000019471 pLKO-puro shTAZ 73 Sigma Mission TRC1 TRCN0000019473 TetO-FUW-pgk-puro ( Chowdhury et al., 2016 ) Addgene #85747; RRID:Addgene_85747 pLVX-Tight-Puro Tet-On Vector Xaralabos Varelas, Boston University, Boston, MA, USA N/A pLVX-TP-3F-TAZ4SA Xaralabos Varelas, Boston University, Boston, MA, USA N/A Scramble control shRNA ( Gu et al, 2016 ) N/A ABL1 shRNA ( Gu et al, 2016 ) N/A ABL2 shRNA ( Gu et al, 2016 ) N/A 3XFlag pCMV5-TOPO TAZ wild type ( Varelas et al., 2008 ) Addgene #24809; RRID:Addgene_24809 3XFlag pCMV5-TOPO TAZ Y321F This paper N/A Tet-pLKO-puro ( Wiederschain et al., 2009 ) Addgene #21915; RRID:Addgene_21915 Tet-pLKO-shNTC-puro This paper N/A Tet-pLKO-shAXL-puro This paper N/A, shAXL clone TRCN0000001040 Tet-pLKO-shTAZ-puro This paper N/A, shTAZ clone TRCN0000019470 N174-MCS http://n2t.net/addgene:81061 Addgene #81061; RRID:Addgene_81061 phL1A-pcDNA3 ( Hlavin and Lemmon, 1991 ) Addgene #12307; RRID:Addgene_12307 N174-L1CAM This paper N/A pN1-eGFP Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP WT Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP R198K This paper N/A pN1-ABL2-eGFP K317M This paper N/A pWZL Neo Myr Flag AXL ( Boehm et al., 2007 ) Addgene #20428; RRID:Addgene_20428 pWZL Neo Myr Flag AXL Y779F This paper N/A pWZL Neo Myr Flag AXL Y821F This paper N/A pWZL Neo Myr Flag AXL Y830F This paper N/A pWZL Neo Myr Flag AXL Y866F This paper N/A Software and Algorithms Prism 6 and 8 Graphpad http://graphpad.com/scientific-software/prism ImageJ ( Schneider et al., 2012 ) http://imagej.nih.gov RStudio R Foundation for Statistical Computing http://rstudio.com CBLigand Online BBB Predictor Tool v0.90 ( Liu et al., 2014 ) http://cbligand.org Living Image Perkin Elmer http://perkinelmer.com GSEA 3.0 ( Subramanian et al., 2005 ) http://software.broadinstitute.org/gsea KM Plotter ( Gyorffy et al., 2013 ) http://kmplot.com CBioPortal v3.1.1 ( Cerami et al., 2012 ; Gao et al., 2013 ) http://cbioportal.org TrimGalore v0.4.4 Babraham Bioinformatics http://github.com/FelixKrueger/TrimGalore STAR aligner ( Dobin et al., 2013 ) http://github.com/alexdobin/STAR HTSeq-count ( Anders et al., 2015 ) http://htseq.readthedocs.io DESeq2 v2.12 ( Love et al., 2014 ) http://bioconductor.org/packages/release/bioc/html/DESeq2.html Hisat2 v2.1.0 ( Kim et al., 2019 ) http://ccb.jhu.edu/software/hisat2/index.shtml Open in a separate window KEY RESOURCES TABLE Co-immunoprecipitation assays. .. Lysates were incubated for 30 min on ice and then cleared by spinning at 15,000 rpm for 10 min. Supernatants were incubated with antibodies overnight followed by incubation with protein A/G PLUS-agarose beads (Santa Cruz) for 3 h. Beads were washed three times with immunoprecipitation buffer afterwards.
Article Title: A TAZ-AXL-ABL2 feed-forward signaling axis promotes lung adenocarcinoma brain metastasis
Article Snippet: .. Recombinant DNA & Plasmids pLKO-puro Non-Target shRNA Control Sigma Mission TRC1 SHC016-1EA pLKO-puro shAXL 1040 Sigma Mission TRC1 TRCN0000001040 pLKO-puro shTAZ 70 Sigma Mission TRC1 TRCN0000019470 pLKO-puro shTAZ 71 Sigma Mission TRC1 TRCN0000019471 pLKO-puro shTAZ 73 Sigma Mission TRC1 TRCN0000019473 TetO-FUW-pgk-puro ( Chowdhury et al., 2016 ) Addgene #85747; RRID:Addgene_85747 pLVX-Tight-Puro Tet-On Vector Xaralabos Varelas, Boston University, Boston, MA, USA N/A pLVX-TP-3F-TAZ4SA Xaralabos Varelas, Boston University, Boston, MA, USA N/A Scramble control shRNA ( Gu et al, 2016 ) N/A ABL1 shRNA ( Gu et al, 2016 ) N/A ABL2 shRNA ( Gu et al, 2016 ) N/A 3XFlag pCMV5-TOPO TAZ wild type ( Varelas et al., 2008 ) Addgene #24809; RRID:Addgene_24809 3XFlag pCMV5-TOPO TAZ Y321F This paper N/A Tet-pLKO-puro ( Wiederschain et al., 2009 ) Addgene #21915; RRID:Addgene_21915 Tet-pLKO-shNTC-puro This paper N/A Tet-pLKO-shAXL-puro This paper N/A, shAXL clone TRCN0000001040 Tet-pLKO-shTAZ-puro This paper N/A, shTAZ clone TRCN0000019470 N174-MCS http://n2t.net/addgene:81061 Addgene #81061; RRID:Addgene_81061 phL1A-pcDNA3 ( Hlavin and Lemmon, 1991 ) Addgene #12307; RRID:Addgene_12307 N174-L1CAM This paper N/A pN1-eGFP Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP WT Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP R198K This paper N/A pN1-ABL2-eGFP K317M This paper N/A pWZL Neo Myr Flag AXL ( Boehm et al., 2007 ) Addgene #20428; RRID:Addgene_20428 pWZL Neo Myr Flag AXL Y779F This paper N/A pWZL Neo Myr Flag AXL Y821F This paper N/A pWZL Neo Myr Flag AXL Y830F This paper N/A pWZL Neo Myr Flag AXL Y866F This paper N/A Software and Algorithms Prism 6 and 8 Graphpad http://graphpad.com/scientific-software/prism ImageJ ( Schneider et al., 2012 ) http://imagej.nih.gov RStudio R Foundation for Statistical Computing http://rstudio.com CBLigand Online BBB Predictor Tool v0.90 ( Liu et al., 2014 ) http://cbligand.org Living Image Perkin Elmer http://perkinelmer.com GSEA 3.0 ( Subramanian et al., 2005 ) http://software.broadinstitute.org/gsea KM Plotter ( Gyorffy et al., 2013 ) http://kmplot.com CBioPortal v3.1.1 ( Cerami et al., 2012 ; Gao et al., 2013 ) http://cbioportal.org TrimGalore v0.4.4 Babraham Bioinformatics http://github.com/FelixKrueger/TrimGalore STAR aligner ( Dobin et al., 2013 ) http://github.com/alexdobin/STAR HTSeq-count ( Anders et al., 2015 ) http://htseq.readthedocs.io DESeq2 v2.12 ( Love et al., 2014 ) http://bioconductor.org/packages/release/bioc/html/DESeq2.html Hisat2 v2.1.0 ( Kim et al., 2019 ) http://ccb.jhu.edu/software/hisat2/index.shtml Open in a separate window KEY RESOURCES TABLE ..
shRNA:Article Title: A TAZ-AXL-ABL2 feed-forward signaling axis promotes lung adenocarcinoma brain metastasis
Article Snippet: Read counts from aligned output files were determined with the Htseq-count tool using reference GTF files obtained from Ensembl. .. Recombinant DNA & Plasmids pLKO-puro Non-Target shRNA Control Sigma Mission TRC1 SHC016-1EA pLKO-puro shAXL 1040 Sigma Mission TRC1 TRCN0000001040 pLKO-puro shTAZ 70 Sigma Mission TRC1 TRCN0000019470 pLKO-puro shTAZ 71 Sigma Mission TRC1 TRCN0000019471 pLKO-puro shTAZ 73 Sigma Mission TRC1 TRCN0000019473 TetO-FUW-pgk-puro ( Chowdhury et al., 2016 ) Addgene #85747; RRID:Addgene_85747 pLVX-Tight-Puro Tet-On Vector Xaralabos Varelas, Boston University, Boston, MA, USA N/A pLVX-TP-3F-TAZ4SA Xaralabos Varelas, Boston University, Boston, MA, USA N/A Scramble control shRNA ( Gu et al, 2016 ) N/A ABL1 shRNA ( Gu et al, 2016 ) N/A ABL2 shRNA ( Gu et al, 2016 ) N/A 3XFlag pCMV5-TOPO TAZ wild type ( Varelas et al., 2008 ) Addgene #24809; RRID:Addgene_24809 3XFlag pCMV5-TOPO TAZ Y321F This paper N/A Tet-pLKO-puro ( Wiederschain et al., 2009 ) Addgene #21915; RRID:Addgene_21915 Tet-pLKO-shNTC-puro This paper N/A Tet-pLKO-shAXL-puro This paper N/A, shAXL clone TRCN0000001040 Tet-pLKO-shTAZ-puro This paper N/A, shTAZ clone TRCN0000019470 N174-MCS http://n2t.net/addgene:81061 Addgene #81061; RRID:Addgene_81061 phL1A-pcDNA3 ( Hlavin and Lemmon, 1991 ) Addgene #12307; RRID:Addgene_12307 N174-L1CAM This paper N/A pN1-eGFP Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP WT Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP R198K This paper N/A pN1-ABL2-eGFP K317M This paper N/A pWZL Neo Myr Flag AXL ( Boehm et al., 2007 ) Addgene #20428; RRID:Addgene_20428 pWZL Neo Myr Flag AXL Y779F This paper N/A pWZL Neo Myr Flag AXL Y821F This paper N/A pWZL Neo Myr Flag AXL Y830F This paper N/A pWZL Neo Myr Flag AXL Y866F This paper N/A Software and Algorithms Prism 6 and 8 Graphpad http://graphpad.com/scientific-software/prism ImageJ ( Schneider et al., 2012 ) http://imagej.nih.gov RStudio R Foundation for Statistical Computing http://rstudio.com CBLigand Online BBB Predictor Tool v0.90 ( Liu et al., 2014 ) http://cbligand.org Living Image Perkin Elmer http://perkinelmer.com GSEA 3.0 ( Subramanian et al., 2005 ) http://software.broadinstitute.org/gsea KM Plotter ( Gyorffy et al., 2013 ) http://kmplot.com CBioPortal v3.1.1 ( Cerami et al., 2012 ; Gao et al., 2013 ) http://cbioportal.org TrimGalore v0.4.4 Babraham Bioinformatics http://github.com/FelixKrueger/TrimGalore STAR aligner ( Dobin et al., 2013 ) http://github.com/alexdobin/STAR HTSeq-count ( Anders et al., 2015 ) http://htseq.readthedocs.io DESeq2 v2.12 ( Love et al., 2014 ) http://bioconductor.org/packages/release/bioc/html/DESeq2.html Hisat2 v2.1.0 ( Kim et al., 2019 ) http://ccb.jhu.edu/software/hisat2/index.shtml Open in a separate window KEY RESOURCES TABLE Co-immunoprecipitation assays. .. Lysates were incubated for 30 min on ice and then cleared by spinning at 15,000 rpm for 10 min. Supernatants were incubated with antibodies overnight followed by incubation with protein A/G PLUS-agarose beads (Santa Cruz) for 3 h. Beads were washed three times with immunoprecipitation buffer afterwards.
Article Title: A TAZ-AXL-ABL2 feed-forward signaling axis promotes lung adenocarcinoma brain metastasis
Article Snippet: .. Recombinant DNA & Plasmids pLKO-puro Non-Target shRNA Control Sigma Mission TRC1 SHC016-1EA pLKO-puro shAXL 1040 Sigma Mission TRC1 TRCN0000001040 pLKO-puro shTAZ 70 Sigma Mission TRC1 TRCN0000019470 pLKO-puro shTAZ 71 Sigma Mission TRC1 TRCN0000019471 pLKO-puro shTAZ 73 Sigma Mission TRC1 TRCN0000019473 TetO-FUW-pgk-puro ( Chowdhury et al., 2016 ) Addgene #85747; RRID:Addgene_85747 pLVX-Tight-Puro Tet-On Vector Xaralabos Varelas, Boston University, Boston, MA, USA N/A pLVX-TP-3F-TAZ4SA Xaralabos Varelas, Boston University, Boston, MA, USA N/A Scramble control shRNA ( Gu et al, 2016 ) N/A ABL1 shRNA ( Gu et al, 2016 ) N/A ABL2 shRNA ( Gu et al, 2016 ) N/A 3XFlag pCMV5-TOPO TAZ wild type ( Varelas et al., 2008 ) Addgene #24809; RRID:Addgene_24809 3XFlag pCMV5-TOPO TAZ Y321F This paper N/A Tet-pLKO-puro ( Wiederschain et al., 2009 ) Addgene #21915; RRID:Addgene_21915 Tet-pLKO-shNTC-puro This paper N/A Tet-pLKO-shAXL-puro This paper N/A, shAXL clone TRCN0000001040 Tet-pLKO-shTAZ-puro This paper N/A, shTAZ clone TRCN0000019470 N174-MCS http://n2t.net/addgene:81061 Addgene #81061; RRID:Addgene_81061 phL1A-pcDNA3 ( Hlavin and Lemmon, 1991 ) Addgene #12307; RRID:Addgene_12307 N174-L1CAM This paper N/A pN1-eGFP Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP WT Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP R198K This paper N/A pN1-ABL2-eGFP K317M This paper N/A pWZL Neo Myr Flag AXL ( Boehm et al., 2007 ) Addgene #20428; RRID:Addgene_20428 pWZL Neo Myr Flag AXL Y779F This paper N/A pWZL Neo Myr Flag AXL Y821F This paper N/A pWZL Neo Myr Flag AXL Y830F This paper N/A pWZL Neo Myr Flag AXL Y866F This paper N/A Software and Algorithms Prism 6 and 8 Graphpad http://graphpad.com/scientific-software/prism ImageJ ( Schneider et al., 2012 ) http://imagej.nih.gov RStudio R Foundation for Statistical Computing http://rstudio.com CBLigand Online BBB Predictor Tool v0.90 ( Liu et al., 2014 ) http://cbligand.org Living Image Perkin Elmer http://perkinelmer.com GSEA 3.0 ( Subramanian et al., 2005 ) http://software.broadinstitute.org/gsea KM Plotter ( Gyorffy et al., 2013 ) http://kmplot.com CBioPortal v3.1.1 ( Cerami et al., 2012 ; Gao et al., 2013 ) http://cbioportal.org TrimGalore v0.4.4 Babraham Bioinformatics http://github.com/FelixKrueger/TrimGalore STAR aligner ( Dobin et al., 2013 ) http://github.com/alexdobin/STAR HTSeq-count ( Anders et al., 2015 ) http://htseq.readthedocs.io DESeq2 v2.12 ( Love et al., 2014 ) http://bioconductor.org/packages/release/bioc/html/DESeq2.html Hisat2 v2.1.0 ( Kim et al., 2019 ) http://ccb.jhu.edu/software/hisat2/index.shtml Open in a separate window KEY RESOURCES TABLE ..
Control:Article Title: A TAZ-AXL-ABL2 feed-forward signaling axis promotes lung adenocarcinoma brain metastasis
Article Snippet: Read counts from aligned output files were determined with the Htseq-count tool using reference GTF files obtained from Ensembl. .. Recombinant DNA & Plasmids pLKO-puro Non-Target shRNA Control Sigma Mission TRC1 SHC016-1EA pLKO-puro shAXL 1040 Sigma Mission TRC1 TRCN0000001040 pLKO-puro shTAZ 70 Sigma Mission TRC1 TRCN0000019470 pLKO-puro shTAZ 71 Sigma Mission TRC1 TRCN0000019471 pLKO-puro shTAZ 73 Sigma Mission TRC1 TRCN0000019473 TetO-FUW-pgk-puro ( Chowdhury et al., 2016 ) Addgene #85747; RRID:Addgene_85747 pLVX-Tight-Puro Tet-On Vector Xaralabos Varelas, Boston University, Boston, MA, USA N/A pLVX-TP-3F-TAZ4SA Xaralabos Varelas, Boston University, Boston, MA, USA N/A Scramble control shRNA ( Gu et al, 2016 ) N/A ABL1 shRNA ( Gu et al, 2016 ) N/A ABL2 shRNA ( Gu et al, 2016 ) N/A 3XFlag pCMV5-TOPO TAZ wild type ( Varelas et al., 2008 ) Addgene #24809; RRID:Addgene_24809 3XFlag pCMV5-TOPO TAZ Y321F This paper N/A Tet-pLKO-puro ( Wiederschain et al., 2009 ) Addgene #21915; RRID:Addgene_21915 Tet-pLKO-shNTC-puro This paper N/A Tet-pLKO-shAXL-puro This paper N/A, shAXL clone TRCN0000001040 Tet-pLKO-shTAZ-puro This paper N/A, shTAZ clone TRCN0000019470 N174-MCS http://n2t.net/addgene:81061 Addgene #81061; RRID:Addgene_81061 phL1A-pcDNA3 ( Hlavin and Lemmon, 1991 ) Addgene #12307; RRID:Addgene_12307 N174-L1CAM This paper N/A pN1-eGFP Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP WT Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP R198K This paper N/A pN1-ABL2-eGFP K317M This paper N/A pWZL Neo Myr Flag AXL ( Boehm et al., 2007 ) Addgene #20428; RRID:Addgene_20428 pWZL Neo Myr Flag AXL Y779F This paper N/A pWZL Neo Myr Flag AXL Y821F This paper N/A pWZL Neo Myr Flag AXL Y830F This paper N/A pWZL Neo Myr Flag AXL Y866F This paper N/A Software and Algorithms Prism 6 and 8 Graphpad http://graphpad.com/scientific-software/prism ImageJ ( Schneider et al., 2012 ) http://imagej.nih.gov RStudio R Foundation for Statistical Computing http://rstudio.com CBLigand Online BBB Predictor Tool v0.90 ( Liu et al., 2014 ) http://cbligand.org Living Image Perkin Elmer http://perkinelmer.com GSEA 3.0 ( Subramanian et al., 2005 ) http://software.broadinstitute.org/gsea KM Plotter ( Gyorffy et al., 2013 ) http://kmplot.com CBioPortal v3.1.1 ( Cerami et al., 2012 ; Gao et al., 2013 ) http://cbioportal.org TrimGalore v0.4.4 Babraham Bioinformatics http://github.com/FelixKrueger/TrimGalore STAR aligner ( Dobin et al., 2013 ) http://github.com/alexdobin/STAR HTSeq-count ( Anders et al., 2015 ) http://htseq.readthedocs.io DESeq2 v2.12 ( Love et al., 2014 ) http://bioconductor.org/packages/release/bioc/html/DESeq2.html Hisat2 v2.1.0 ( Kim et al., 2019 ) http://ccb.jhu.edu/software/hisat2/index.shtml Open in a separate window KEY RESOURCES TABLE Co-immunoprecipitation assays. .. Lysates were incubated for 30 min on ice and then cleared by spinning at 15,000 rpm for 10 min. Supernatants were incubated with antibodies overnight followed by incubation with protein A/G PLUS-agarose beads (Santa Cruz) for 3 h. Beads were washed three times with immunoprecipitation buffer afterwards.
Article Title: A TAZ-AXL-ABL2 feed-forward signaling axis promotes lung adenocarcinoma brain metastasis
Article Snippet: .. Recombinant DNA & Plasmids pLKO-puro Non-Target shRNA Control Sigma Mission TRC1 SHC016-1EA pLKO-puro shAXL 1040 Sigma Mission TRC1 TRCN0000001040 pLKO-puro shTAZ 70 Sigma Mission TRC1 TRCN0000019470 pLKO-puro shTAZ 71 Sigma Mission TRC1 TRCN0000019471 pLKO-puro shTAZ 73 Sigma Mission TRC1 TRCN0000019473 TetO-FUW-pgk-puro ( Chowdhury et al., 2016 ) Addgene #85747; RRID:Addgene_85747 pLVX-Tight-Puro Tet-On Vector Xaralabos Varelas, Boston University, Boston, MA, USA N/A pLVX-TP-3F-TAZ4SA Xaralabos Varelas, Boston University, Boston, MA, USA N/A Scramble control shRNA ( Gu et al, 2016 ) N/A ABL1 shRNA ( Gu et al, 2016 ) N/A ABL2 shRNA ( Gu et al, 2016 ) N/A 3XFlag pCMV5-TOPO TAZ wild type ( Varelas et al., 2008 ) Addgene #24809; RRID:Addgene_24809 3XFlag pCMV5-TOPO TAZ Y321F This paper N/A Tet-pLKO-puro ( Wiederschain et al., 2009 ) Addgene #21915; RRID:Addgene_21915 Tet-pLKO-shNTC-puro This paper N/A Tet-pLKO-shAXL-puro This paper N/A, shAXL clone TRCN0000001040 Tet-pLKO-shTAZ-puro This paper N/A, shTAZ clone TRCN0000019470 N174-MCS http://n2t.net/addgene:81061 Addgene #81061; RRID:Addgene_81061 phL1A-pcDNA3 ( Hlavin and Lemmon, 1991 ) Addgene #12307; RRID:Addgene_12307 N174-L1CAM This paper N/A pN1-eGFP Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP WT Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP R198K This paper N/A pN1-ABL2-eGFP K317M This paper N/A pWZL Neo Myr Flag AXL ( Boehm et al., 2007 ) Addgene #20428; RRID:Addgene_20428 pWZL Neo Myr Flag AXL Y779F This paper N/A pWZL Neo Myr Flag AXL Y821F This paper N/A pWZL Neo Myr Flag AXL Y830F This paper N/A pWZL Neo Myr Flag AXL Y866F This paper N/A Software and Algorithms Prism 6 and 8 Graphpad http://graphpad.com/scientific-software/prism ImageJ ( Schneider et al., 2012 ) http://imagej.nih.gov RStudio R Foundation for Statistical Computing http://rstudio.com CBLigand Online BBB Predictor Tool v0.90 ( Liu et al., 2014 ) http://cbligand.org Living Image Perkin Elmer http://perkinelmer.com GSEA 3.0 ( Subramanian et al., 2005 ) http://software.broadinstitute.org/gsea KM Plotter ( Gyorffy et al., 2013 ) http://kmplot.com CBioPortal v3.1.1 ( Cerami et al., 2012 ; Gao et al., 2013 ) http://cbioportal.org TrimGalore v0.4.4 Babraham Bioinformatics http://github.com/FelixKrueger/TrimGalore STAR aligner ( Dobin et al., 2013 ) http://github.com/alexdobin/STAR HTSeq-count ( Anders et al., 2015 ) http://htseq.readthedocs.io DESeq2 v2.12 ( Love et al., 2014 ) http://bioconductor.org/packages/release/bioc/html/DESeq2.html Hisat2 v2.1.0 ( Kim et al., 2019 ) http://ccb.jhu.edu/software/hisat2/index.shtml Open in a separate window KEY RESOURCES TABLE ..
Software:Article Title: A TAZ-AXL-ABL2 feed-forward signaling axis promotes lung adenocarcinoma brain metastasis
Article Snippet: Read counts from aligned output files were determined with the Htseq-count tool using reference GTF files obtained from Ensembl. .. Recombinant DNA & Plasmids pLKO-puro Non-Target shRNA Control Sigma Mission TRC1 SHC016-1EA pLKO-puro shAXL 1040 Sigma Mission TRC1 TRCN0000001040 pLKO-puro shTAZ 70 Sigma Mission TRC1 TRCN0000019470 pLKO-puro shTAZ 71 Sigma Mission TRC1 TRCN0000019471 pLKO-puro shTAZ 73 Sigma Mission TRC1 TRCN0000019473 TetO-FUW-pgk-puro ( Chowdhury et al., 2016 ) Addgene #85747; RRID:Addgene_85747 pLVX-Tight-Puro Tet-On Vector Xaralabos Varelas, Boston University, Boston, MA, USA N/A pLVX-TP-3F-TAZ4SA Xaralabos Varelas, Boston University, Boston, MA, USA N/A Scramble control shRNA ( Gu et al, 2016 ) N/A ABL1 shRNA ( Gu et al, 2016 ) N/A ABL2 shRNA ( Gu et al, 2016 ) N/A 3XFlag pCMV5-TOPO TAZ wild type ( Varelas et al., 2008 ) Addgene #24809; RRID:Addgene_24809 3XFlag pCMV5-TOPO TAZ Y321F This paper N/A Tet-pLKO-puro ( Wiederschain et al., 2009 ) Addgene #21915; RRID:Addgene_21915 Tet-pLKO-shNTC-puro This paper N/A Tet-pLKO-shAXL-puro This paper N/A, shAXL clone TRCN0000001040 Tet-pLKO-shTAZ-puro This paper N/A, shTAZ clone TRCN0000019470 N174-MCS http://n2t.net/addgene:81061 Addgene #81061; RRID:Addgene_81061 phL1A-pcDNA3 ( Hlavin and Lemmon, 1991 ) Addgene #12307; RRID:Addgene_12307 N174-L1CAM This paper N/A pN1-eGFP Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP WT Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP R198K This paper N/A pN1-ABL2-eGFP K317M This paper N/A pWZL Neo Myr Flag AXL ( Boehm et al., 2007 ) Addgene #20428; RRID:Addgene_20428 pWZL Neo Myr Flag AXL Y779F This paper N/A pWZL Neo Myr Flag AXL Y821F This paper N/A pWZL Neo Myr Flag AXL Y830F This paper N/A pWZL Neo Myr Flag AXL Y866F This paper N/A Software and Algorithms Prism 6 and 8 Graphpad http://graphpad.com/scientific-software/prism ImageJ ( Schneider et al., 2012 ) http://imagej.nih.gov RStudio R Foundation for Statistical Computing http://rstudio.com CBLigand Online BBB Predictor Tool v0.90 ( Liu et al., 2014 ) http://cbligand.org Living Image Perkin Elmer http://perkinelmer.com GSEA 3.0 ( Subramanian et al., 2005 ) http://software.broadinstitute.org/gsea KM Plotter ( Gyorffy et al., 2013 ) http://kmplot.com CBioPortal v3.1.1 ( Cerami et al., 2012 ; Gao et al., 2013 ) http://cbioportal.org TrimGalore v0.4.4 Babraham Bioinformatics http://github.com/FelixKrueger/TrimGalore STAR aligner ( Dobin et al., 2013 ) http://github.com/alexdobin/STAR HTSeq-count ( Anders et al., 2015 ) http://htseq.readthedocs.io DESeq2 v2.12 ( Love et al., 2014 ) http://bioconductor.org/packages/release/bioc/html/DESeq2.html Hisat2 v2.1.0 ( Kim et al., 2019 ) http://ccb.jhu.edu/software/hisat2/index.shtml Open in a separate window KEY RESOURCES TABLE Co-immunoprecipitation assays. .. Lysates were incubated for 30 min on ice and then cleared by spinning at 15,000 rpm for 10 min. Supernatants were incubated with antibodies overnight followed by incubation with protein A/G PLUS-agarose beads (Santa Cruz) for 3 h. Beads were washed three times with immunoprecipitation buffer afterwards.
Article Title: A TAZ-AXL-ABL2 feed-forward signaling axis promotes lung adenocarcinoma brain metastasis
Article Snippet: .. Recombinant DNA & Plasmids pLKO-puro Non-Target shRNA Control Sigma Mission TRC1 SHC016-1EA pLKO-puro shAXL 1040 Sigma Mission TRC1 TRCN0000001040 pLKO-puro shTAZ 70 Sigma Mission TRC1 TRCN0000019470 pLKO-puro shTAZ 71 Sigma Mission TRC1 TRCN0000019471 pLKO-puro shTAZ 73 Sigma Mission TRC1 TRCN0000019473 TetO-FUW-pgk-puro ( Chowdhury et al., 2016 ) Addgene #85747; RRID:Addgene_85747 pLVX-Tight-Puro Tet-On Vector Xaralabos Varelas, Boston University, Boston, MA, USA N/A pLVX-TP-3F-TAZ4SA Xaralabos Varelas, Boston University, Boston, MA, USA N/A Scramble control shRNA ( Gu et al, 2016 ) N/A ABL1 shRNA ( Gu et al, 2016 ) N/A ABL2 shRNA ( Gu et al, 2016 ) N/A 3XFlag pCMV5-TOPO TAZ wild type ( Varelas et al., 2008 ) Addgene #24809; RRID:Addgene_24809 3XFlag pCMV5-TOPO TAZ Y321F This paper N/A Tet-pLKO-puro ( Wiederschain et al., 2009 ) Addgene #21915; RRID:Addgene_21915 Tet-pLKO-shNTC-puro This paper N/A Tet-pLKO-shAXL-puro This paper N/A, shAXL clone TRCN0000001040 Tet-pLKO-shTAZ-puro This paper N/A, shTAZ clone TRCN0000019470 N174-MCS http://n2t.net/addgene:81061 Addgene #81061; RRID:Addgene_81061 phL1A-pcDNA3 ( Hlavin and Lemmon, 1991 ) Addgene #12307; RRID:Addgene_12307 N174-L1CAM This paper N/A pN1-eGFP Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP WT Anthony Koleske, Yale University, New Haven, CT, USA N/A pN1-ABL2-eGFP R198K This paper N/A pN1-ABL2-eGFP K317M This paper N/A pWZL Neo Myr Flag AXL ( Boehm et al., 2007 ) Addgene #20428; RRID:Addgene_20428 pWZL Neo Myr Flag AXL Y779F This paper N/A pWZL Neo Myr Flag AXL Y821F This paper N/A pWZL Neo Myr Flag AXL Y830F This paper N/A pWZL Neo Myr Flag AXL Y866F This paper N/A Software and Algorithms Prism 6 and 8 Graphpad http://graphpad.com/scientific-software/prism ImageJ ( Schneider et al., 2012 ) http://imagej.nih.gov RStudio R Foundation for Statistical Computing http://rstudio.com CBLigand Online BBB Predictor Tool v0.90 ( Liu et al., 2014 ) http://cbligand.org Living Image Perkin Elmer http://perkinelmer.com GSEA 3.0 ( Subramanian et al., 2005 ) http://software.broadinstitute.org/gsea KM Plotter ( Gyorffy et al., 2013 ) http://kmplot.com CBioPortal v3.1.1 ( Cerami et al., 2012 ; Gao et al., 2013 ) http://cbioportal.org TrimGalore v0.4.4 Babraham Bioinformatics http://github.com/FelixKrueger/TrimGalore STAR aligner ( Dobin et al., 2013 ) http://github.com/alexdobin/STAR HTSeq-count ( Anders et al., 2015 ) http://htseq.readthedocs.io DESeq2 v2.12 ( Love et al., 2014 ) http://bioconductor.org/packages/release/bioc/html/DESeq2.html Hisat2 v2.1.0 ( Kim et al., 2019 ) http://ccb.jhu.edu/software/hisat2/index.shtml Open in a separate window KEY RESOURCES TABLE ..
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