Immunohistochemistry:Article Title: Haploinsufficient phenotypes promote selection of PTEN and ARID1A-deficient clones in human colon.
Article Snippet: Reagent/resource Reference or source Identifier or catalogue number Additional antibody info: Titre IHC/Wes MAOA Mouse Santa Cruz SC-271123 1:200 MCM2 Mouse BioRad MCA1859 1:500 MUC2 Rabbit Santa Cruz SC-15334 1:400 p-Akt Rabbit Cell Signalling 4060 1:100 pH3 Mouse Cell Signalling 9706 1:500 PTEN Rabbit Cell Signalling 9559 1:300, 1:50 PTEN Mouse Sigma 04-035 1:200 SMAD4 Mouse Santa Cruz sc-7966 1:150 SMAD4 Rabbit Abcam ab217267 1:400 SOX9 Mouse Atlas CAB068240 1:800 STAG2 Goat LS-Bio LS-B11284 1:1000 TCF7L2 Atlas 34-3800/ CAB013535 1:200 TCF7L2 Rabbit Scientific Laboratory Supplies SAB1404454 1:50 Secondary HRP for TSA amplification Mouse Thermo Fisher T20916 1:200 Secondary HRP for TSA amplification Rabbit Thermo Fisher 65-6120 1:200 Secondary HRP for TSA amplification Goat Thermo Fisher A15999 1:200 Oligonucleotides and other sequence-based reagents Fluidigm Primers This Study Appendix Table S3,4 Software ICE Synthego https:// ice.synthego.com/ Halo Indica Labs https:// indicalab.com/halo/ QuPath https:// qupath.github.io/ RHclones package https://github.com/ ElEd2/RHClones Amplicon Seq pipeline https://github.com/ crukcibioinformatics/ ampliconseq Other TSA Reagent Cy5 Akoya TS-000203 TSA Reagent Cy3 Akoya TS-000204 TSA Reagent Alexa Fluorophore 488 Thermo Fisher B40953 Opal 6-colour manual detection kit Akoya NEL811001KT CD45 (Intracellular Domain) (D9M8I) and CO-0013-488 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 81757 Reagent/resource Reference or source Identifier or catalogue number Additional antibody info: Titre IHC/Wes CD3ε (D7A6ETM) and CO-0001-594 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 84634 CD11c (D3V1E) and CO-0017-647 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 96411 CD11b/ITGAM (D6X1N) and CO0037-750 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 67799 CD68 (D4B9C) and CO-0007-488 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 73071 CD163 (D6U1J) and CO-0022-594 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 43547 TIM3 (D5D5RTM) and CO-0010-647 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 15231 Vimentin (D21H3) and CO-0012-750 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 61002 SignalStarTM Midplex IHC Buffer Kit Cell Signalling Technologies 29414 Arcturus PicoPure DNA extraction kit Thermo Fisher KIT0103 LP 8.8.6 integrated fluidic circuit (IFC) Fluidigm 101-7663 IVF EZ-Grip pipette Cooper Surgical 7-72-2800 and 7- 72-2155/1, 7-72- 2200/1, 7-72- 2290/1 for tips
Amplification:Article Title: Haploinsufficient phenotypes promote selection of PTEN and ARID1A-deficient clones in human colon.
Article Snippet: Reagent/resource Reference or source Identifier or catalogue number Additional antibody info: Titre IHC/Wes MAOA Mouse Santa Cruz SC-271123 1:200 MCM2 Mouse BioRad MCA1859 1:500 MUC2 Rabbit Santa Cruz SC-15334 1:400 p-Akt Rabbit Cell Signalling 4060 1:100 pH3 Mouse Cell Signalling 9706 1:500 PTEN Rabbit Cell Signalling 9559 1:300, 1:50 PTEN Mouse Sigma 04-035 1:200 SMAD4 Mouse Santa Cruz sc-7966 1:150 SMAD4 Rabbit Abcam ab217267 1:400 SOX9 Mouse Atlas CAB068240 1:800 STAG2 Goat LS-Bio LS-B11284 1:1000 TCF7L2 Atlas 34-3800/ CAB013535 1:200 TCF7L2 Rabbit Scientific Laboratory Supplies SAB1404454 1:50 Secondary HRP for TSA amplification Mouse Thermo Fisher T20916 1:200 Secondary HRP for TSA amplification Rabbit Thermo Fisher 65-6120 1:200 Secondary HRP for TSA amplification Goat Thermo Fisher A15999 1:200 Oligonucleotides and other sequence-based reagents Fluidigm Primers This Study Appendix Table S3,4 Software ICE Synthego https:// ice.synthego.com/ Halo Indica Labs https:// indicalab.com/halo/ QuPath https:// qupath.github.io/ RHclones package https://github.com/ ElEd2/RHClones Amplicon Seq pipeline https://github.com/ crukcibioinformatics/ ampliconseq Other TSA Reagent Cy5 Akoya TS-000203 TSA Reagent Cy3 Akoya TS-000204 TSA Reagent Alexa Fluorophore 488 Thermo Fisher B40953 Opal 6-colour manual detection kit Akoya NEL811001KT CD45 (Intracellular Domain) (D9M8I) and CO-0013-488 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 81757 Reagent/resource Reference or source Identifier or catalogue number Additional antibody info: Titre IHC/Wes CD3ε (D7A6ETM) and CO-0001-594 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 84634 CD11c (D3V1E) and CO-0017-647 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 96411 CD11b/ITGAM (D6X1N) and CO0037-750 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 67799 CD68 (D4B9C) and CO-0007-488 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 73071 CD163 (D6U1J) and CO-0022-594 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 43547 TIM3 (D5D5RTM) and CO-0010-647 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 15231 Vimentin (D21H3) and CO-0012-750 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 61002 SignalStarTM Midplex IHC Buffer Kit Cell Signalling Technologies 29414 Arcturus PicoPure DNA extraction kit Thermo Fisher KIT0103 LP 8.8.6 integrated fluidic circuit (IFC) Fluidigm 101-7663 IVF EZ-Grip pipette Cooper Surgical 7-72-2800 and 7- 72-2155/1, 7-72- 2200/1, 7-72- 2290/1 for tips
Sequencing:Article Title: Haploinsufficient phenotypes promote selection of PTEN and ARID1A-deficient clones in human colon.
Article Snippet: Reagent/resource Reference or source Identifier or catalogue number Additional antibody info: Titre IHC/Wes MAOA Mouse Santa Cruz SC-271123 1:200 MCM2 Mouse BioRad MCA1859 1:500 MUC2 Rabbit Santa Cruz SC-15334 1:400 p-Akt Rabbit Cell Signalling 4060 1:100 pH3 Mouse Cell Signalling 9706 1:500 PTEN Rabbit Cell Signalling 9559 1:300, 1:50 PTEN Mouse Sigma 04-035 1:200 SMAD4 Mouse Santa Cruz sc-7966 1:150 SMAD4 Rabbit Abcam ab217267 1:400 SOX9 Mouse Atlas CAB068240 1:800 STAG2 Goat LS-Bio LS-B11284 1:1000 TCF7L2 Atlas 34-3800/ CAB013535 1:200 TCF7L2 Rabbit Scientific Laboratory Supplies SAB1404454 1:50 Secondary HRP for TSA amplification Mouse Thermo Fisher T20916 1:200 Secondary HRP for TSA amplification Rabbit Thermo Fisher 65-6120 1:200 Secondary HRP for TSA amplification Goat Thermo Fisher A15999 1:200 Oligonucleotides and other sequence-based reagents Fluidigm Primers This Study Appendix Table S3,4 Software ICE Synthego https:// ice.synthego.com/ Halo Indica Labs https:// indicalab.com/halo/ QuPath https:// qupath.github.io/ RHclones package https://github.com/ ElEd2/RHClones Amplicon Seq pipeline https://github.com/ crukcibioinformatics/ ampliconseq Other TSA Reagent Cy5 Akoya TS-000203 TSA Reagent Cy3 Akoya TS-000204 TSA Reagent Alexa Fluorophore 488 Thermo Fisher B40953 Opal 6-colour manual detection kit Akoya NEL811001KT CD45 (Intracellular Domain) (D9M8I) and CO-0013-488 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 81757 Reagent/resource Reference or source Identifier or catalogue number Additional antibody info: Titre IHC/Wes CD3ε (D7A6ETM) and CO-0001-594 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 84634 CD11c (D3V1E) and CO-0017-647 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 96411 CD11b/ITGAM (D6X1N) and CO0037-750 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 67799 CD68 (D4B9C) and CO-0007-488 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 73071 CD163 (D6U1J) and CO-0022-594 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 43547 TIM3 (D5D5RTM) and CO-0010-647 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 15231 Vimentin (D21H3) and CO-0012-750 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 61002 SignalStarTM Midplex IHC Buffer Kit Cell Signalling Technologies 29414 Arcturus PicoPure DNA extraction kit Thermo Fisher KIT0103 LP 8.8.6 integrated fluidic circuit (IFC) Fluidigm 101-7663 IVF EZ-Grip pipette Cooper Surgical 7-72-2800 and 7- 72-2155/1, 7-72- 2200/1, 7-72- 2290/1 for tips
Software:Article Title: Haploinsufficient phenotypes promote selection of PTEN and ARID1A-deficient clones in human colon.
Article Snippet: Reagent/resource Reference or source Identifier or catalogue number Additional antibody info: Titre IHC/Wes MAOA Mouse Santa Cruz SC-271123 1:200 MCM2 Mouse BioRad MCA1859 1:500 MUC2 Rabbit Santa Cruz SC-15334 1:400 p-Akt Rabbit Cell Signalling 4060 1:100 pH3 Mouse Cell Signalling 9706 1:500 PTEN Rabbit Cell Signalling 9559 1:300, 1:50 PTEN Mouse Sigma 04-035 1:200 SMAD4 Mouse Santa Cruz sc-7966 1:150 SMAD4 Rabbit Abcam ab217267 1:400 SOX9 Mouse Atlas CAB068240 1:800 STAG2 Goat LS-Bio LS-B11284 1:1000 TCF7L2 Atlas 34-3800/ CAB013535 1:200 TCF7L2 Rabbit Scientific Laboratory Supplies SAB1404454 1:50 Secondary HRP for TSA amplification Mouse Thermo Fisher T20916 1:200 Secondary HRP for TSA amplification Rabbit Thermo Fisher 65-6120 1:200 Secondary HRP for TSA amplification Goat Thermo Fisher A15999 1:200 Oligonucleotides and other sequence-based reagents Fluidigm Primers This Study Appendix Table S3,4 Software ICE Synthego https:// ice.synthego.com/ Halo Indica Labs https:// indicalab.com/halo/ QuPath https:// qupath.github.io/ RHclones package https://github.com/ ElEd2/RHClones Amplicon Seq pipeline https://github.com/ crukcibioinformatics/ ampliconseq Other TSA Reagent Cy5 Akoya TS-000203 TSA Reagent Cy3 Akoya TS-000204 TSA Reagent Alexa Fluorophore 488 Thermo Fisher B40953 Opal 6-colour manual detection kit Akoya NEL811001KT CD45 (Intracellular Domain) (D9M8I) and CO-0013-488 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 81757 Reagent/resource Reference or source Identifier or catalogue number Additional antibody info: Titre IHC/Wes CD3ε (D7A6ETM) and CO-0001-594 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 84634 CD11c (D3V1E) and CO-0017-647 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 96411 CD11b/ITGAM (D6X1N) and CO0037-750 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 67799 CD68 (D4B9C) and CO-0007-488 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 73071 CD163 (D6U1J) and CO-0022-594 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 43547 TIM3 (D5D5RTM) and CO-0010-647 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 15231 Vimentin (D21H3) and CO-0012-750 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 61002 SignalStarTM Midplex IHC Buffer Kit Cell Signalling Technologies 29414 Arcturus PicoPure DNA extraction kit Thermo Fisher KIT0103 LP 8.8.6 integrated fluidic circuit (IFC) Fluidigm 101-7663 IVF EZ-Grip pipette Cooper Surgical 7-72-2800 and 7- 72-2155/1, 7-72- 2200/1, 7-72- 2290/1 for tips
DNA Extraction:Article Title: Haploinsufficient phenotypes promote selection of PTEN and ARID1A-deficient clones in human colon.
Article Snippet: Reagent/resource Reference or source Identifier or catalogue number Additional antibody info: Titre IHC/Wes MAOA Mouse Santa Cruz SC-271123 1:200 MCM2 Mouse BioRad MCA1859 1:500 MUC2 Rabbit Santa Cruz SC-15334 1:400 p-Akt Rabbit Cell Signalling 4060 1:100 pH3 Mouse Cell Signalling 9706 1:500 PTEN Rabbit Cell Signalling 9559 1:300, 1:50 PTEN Mouse Sigma 04-035 1:200 SMAD4 Mouse Santa Cruz sc-7966 1:150 SMAD4 Rabbit Abcam ab217267 1:400 SOX9 Mouse Atlas CAB068240 1:800 STAG2 Goat LS-Bio LS-B11284 1:1000 TCF7L2 Atlas 34-3800/ CAB013535 1:200 TCF7L2 Rabbit Scientific Laboratory Supplies SAB1404454 1:50 Secondary HRP for TSA amplification Mouse Thermo Fisher T20916 1:200 Secondary HRP for TSA amplification Rabbit Thermo Fisher 65-6120 1:200 Secondary HRP for TSA amplification Goat Thermo Fisher A15999 1:200 Oligonucleotides and other sequence-based reagents Fluidigm Primers This Study Appendix Table S3,4 Software ICE Synthego https:// ice.synthego.com/ Halo Indica Labs https:// indicalab.com/halo/ QuPath https:// qupath.github.io/ RHclones package https://github.com/ ElEd2/RHClones Amplicon Seq pipeline https://github.com/ crukcibioinformatics/ ampliconseq Other TSA Reagent Cy5 Akoya TS-000203 TSA Reagent Cy3 Akoya TS-000204 TSA Reagent Alexa Fluorophore 488 Thermo Fisher B40953 Opal 6-colour manual detection kit Akoya NEL811001KT CD45 (Intracellular Domain) (D9M8I) and CO-0013-488 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 81757 Reagent/resource Reference or source Identifier or catalogue number Additional antibody info: Titre IHC/Wes CD3ε (D7A6ETM) and CO-0001-594 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 84634 CD11c (D3V1E) and CO-0017-647 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 96411 CD11b/ITGAM (D6X1N) and CO0037-750 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 67799 CD68 (D4B9C) and CO-0007-488 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 73071 CD163 (D6U1J) and CO-0022-594 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 43547 TIM3 (D5D5RTM) and CO-0010-647 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 15231 Vimentin (D21H3) and CO-0012-750 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 61002 SignalStarTM Midplex IHC Buffer Kit Cell Signalling Technologies 29414 Arcturus PicoPure DNA extraction kit Thermo Fisher KIT0103 LP 8.8.6 integrated fluidic circuit (IFC) Fluidigm 101-7663 IVF EZ-Grip pipette Cooper Surgical 7-72-2800 and 7- 72-2155/1, 7-72- 2200/1, 7-72- 2290/1 for tips
Transferring:Article Title: Haploinsufficient phenotypes promote selection of PTEN and ARID1A-deficient clones in human colon.
Article Snippet: Reagent/resource Reference or source Identifier or catalogue number Additional antibody info: Titre IHC/Wes MAOA Mouse Santa Cruz SC-271123 1:200 MCM2 Mouse BioRad MCA1859 1:500 MUC2 Rabbit Santa Cruz SC-15334 1:400 p-Akt Rabbit Cell Signalling 4060 1:100 pH3 Mouse Cell Signalling 9706 1:500 PTEN Rabbit Cell Signalling 9559 1:300, 1:50 PTEN Mouse Sigma 04-035 1:200 SMAD4 Mouse Santa Cruz sc-7966 1:150 SMAD4 Rabbit Abcam ab217267 1:400 SOX9 Mouse Atlas CAB068240 1:800 STAG2 Goat LS-Bio LS-B11284 1:1000 TCF7L2 Atlas 34-3800/ CAB013535 1:200 TCF7L2 Rabbit Scientific Laboratory Supplies SAB1404454 1:50 Secondary HRP for TSA amplification Mouse Thermo Fisher T20916 1:200 Secondary HRP for TSA amplification Rabbit Thermo Fisher 65-6120 1:200 Secondary HRP for TSA amplification Goat Thermo Fisher A15999 1:200 Oligonucleotides and other sequence-based reagents Fluidigm Primers This Study Appendix Table S3,4 Software ICE Synthego https:// ice.synthego.com/ Halo Indica Labs https:// indicalab.com/halo/ QuPath https:// qupath.github.io/ RHclones package https://github.com/ ElEd2/RHClones Amplicon Seq pipeline https://github.com/ crukcibioinformatics/ ampliconseq Other TSA Reagent Cy5 Akoya TS-000203 TSA Reagent Cy3 Akoya TS-000204 TSA Reagent Alexa Fluorophore 488 Thermo Fisher B40953 Opal 6-colour manual detection kit Akoya NEL811001KT CD45 (Intracellular Domain) (D9M8I) and CO-0013-488 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 81757 Reagent/resource Reference or source Identifier or catalogue number Additional antibody info: Titre IHC/Wes CD3ε (D7A6ETM) and CO-0001-594 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 84634 CD11c (D3V1E) and CO-0017-647 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 96411 CD11b/ITGAM (D6X1N) and CO0037-750 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 67799 CD68 (D4B9C) and CO-0007-488 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 73071 CD163 (D6U1J) and CO-0022-594 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 43547 TIM3 (D5D5RTM) and CO-0010-647 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 15231 Vimentin (D21H3) and CO-0012-750 SignalStarTM OligoAntibody Pair Cell Signalling Technologies 61002 SignalStarTM Midplex IHC Buffer Kit Cell Signalling Technologies 29414 Arcturus PicoPure DNA extraction kit Thermo Fisher KIT0103 LP 8.8.6 integrated fluidic circuit (IFC) Fluidigm 101-7663 IVF EZ-Grip pipette Cooper Surgical 7-72-2800 and 7- 72-2155/1, 7-72- 2200/1, 7-72- 2290/1 for tips
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