Cloning:Article Title: Endoplasmic reticulum stress activates human IRE1α through reversible assembly of inactive dimers into small oligomers
Article Snippet: .. Reagent type (species) or resource Designation Source or reference Identifiers Additional information Gene (Homo sapiens) ERN1 HUGO Gene Nomenclature Committee HGNC:3,449 Gene encoding human IRE1a Strain, strain background (Escherichia coli) Stellar Competent Cells Takara Bio 636,763 High- efficiency competent cells for cloning Cell line (Homo- sapiens) U- 2 OS WT Flp- In T- REx Ivan Dikic lab; verified by ATCC STR service; published in Belyy et al., 2020 PWM253 Parental line for all cells in this study, denoted as “WT” Cell line (Homo- sapiens) U- 2 OS IRE1α KO Belyy et al., 2020 PWM254 CRISPR knock- out of IRE1α in PWM253 Cell line (Homo- sapiens) U- 2 OS IRE1α partial KO This paper PWM359 Partial CRISPR knock- out of IRE1α in PWM253, containing one intact ERN1 allele Cell line (Homo- sapiens) U- 2 OS IRE1a- HaloTag endogenously tagged This paper PWM360 Introduction of a C- terminal HaloTag into the endogenous ERN1 locus of PWM359 cells. ..
CRISPR:Article Title: Endoplasmic reticulum stress activates human IRE1α through reversible assembly of inactive dimers into small oligomers
Article Snippet: .. Reagent type (species) or resource Designation Source or reference Identifiers Additional information Gene (Homo sapiens) ERN1 HUGO Gene Nomenclature Committee HGNC:3,449 Gene encoding human IRE1a Strain, strain background (Escherichia coli) Stellar Competent Cells Takara Bio 636,763 High- efficiency competent cells for cloning Cell line (Homo- sapiens) U- 2 OS WT Flp- In T- REx Ivan Dikic lab; verified by ATCC STR service; published in Belyy et al., 2020 PWM253 Parental line for all cells in this study, denoted as “WT” Cell line (Homo- sapiens) U- 2 OS IRE1α KO Belyy et al., 2020 PWM254 CRISPR knock- out of IRE1α in PWM253 Cell line (Homo- sapiens) U- 2 OS IRE1α partial KO This paper PWM359 Partial CRISPR knock- out of IRE1α in PWM253, containing one intact ERN1 allele Cell line (Homo- sapiens) U- 2 OS IRE1a- HaloTag endogenously tagged This paper PWM360 Introduction of a C- terminal HaloTag into the endogenous ERN1 locus of PWM359 cells. ..
Knock-Out:Article Title: Endoplasmic reticulum stress activates human IRE1α through reversible assembly of inactive dimers into small oligomers
Article Snippet: .. Reagent type (species) or resource Designation Source or reference Identifiers Additional information Gene (Homo sapiens) ERN1 HUGO Gene Nomenclature Committee HGNC:3,449 Gene encoding human IRE1a Strain, strain background (Escherichia coli) Stellar Competent Cells Takara Bio 636,763 High- efficiency competent cells for cloning Cell line (Homo- sapiens) U- 2 OS WT Flp- In T- REx Ivan Dikic lab; verified by ATCC STR service; published in Belyy et al., 2020 PWM253 Parental line for all cells in this study, denoted as “WT” Cell line (Homo- sapiens) U- 2 OS IRE1α KO Belyy et al., 2020 PWM254 CRISPR knock- out of IRE1α in PWM253 Cell line (Homo- sapiens) U- 2 OS IRE1α partial KO This paper PWM359 Partial CRISPR knock- out of IRE1α in PWM253, containing one intact ERN1 allele Cell line (Homo- sapiens) U- 2 OS IRE1a- HaloTag endogenously tagged This paper PWM360 Introduction of a C- terminal HaloTag into the endogenous ERN1 locus of PWM359 cells. ..
Article Title: Myopalladin knockout mice develop cardiac dilation and show a maladaptive response to mechanical pressure overload
Article Snippet: .. (species) or resource Designation Source or reference Identifiers Additional information Strain, strain background (male Mus musculus) MYPN knockout (MKO) mice (in C57BL/6 J background) Filomena et al., 2020 N/A Strain, strain background (Mus musculus) C57BL/6 J The Jackson Laboratories Cat# 000664 RRID:IMSR_ JAX:000664 Strain, strain background (Escherichia coli) DH5α electrocompetent cells New England BioLabs Cat# C2989K Strain, strain background (Escherichia coli) BL21- CodonPlus (DE3)RIPL strain Agilent Technologies Cat# 230280 Strain, strain background (Saccharomyces cerevisiae) Y2H Gold yeast strain Takara Bio Cat# 630498 Strain, strain background (Saccharomyces cerevisiae) L40 yeast strain Takara Bio N/A Antibody Anti- MYPN (rabbit polyclonal) Yamamoto et al., 2013 N/A WB (1:1000) Antibody Anti- PALLD 621 (rabbit polyclonal) Pogue- Geile et al., 2006 Kindly provided by Prof. Carol Otey, University of North Carolina, Chapel Hill, NC, USA WB (1:500) IF (1:30) Antibody Anti- NEBL (rabbit polyclonal) Mastrototaro et al., 2015 N/A WB (1:500) Antibody Anti- ANKRD1/CARP (rabbit polyclonal) Miller et al., 2003 N/A WB (1:200) IF (1:20) Antibody Anti- Cypher (rabbit polyclonal) Zhou et al., 2001 Kindly provided by Prof. Ju Chen, University of California San Diego, La Jolla, CA, USA WB (1:500) IF (1:50) Antibody Anti-α-actinin (mouse monoclonal) Merck Life Science Cat# A7811 RRID:AB_476766 WB (1:50000) IF (1:250) Antibody Anti- desmin (rabbit polyclonal) Abcam Cat# Ab8592 RRID:AB_306653 IF (1:80) Antibody Anti- MKL1/MRTF- A (rabbit polyclonal) Merck Life Science Cat# AV37504 RRID:AB_1853972 IF (1:30) Antibody Anti- MKL1/MRTF- A (rabbit polyclonal) Immunological Sciences Cat# AB- 84312 RRID:AB_2892156 WB (1:500) Antibody Anti- desmoplakin 1/2 (mouse monoclonal) Bio- Rad Laboratories Cat# 2722–5204 RRID:AB_619950 WB (1:750) Antibody Anti-α-E- catenin (mouse monoclonal) Santa Cruz Biotechnology Cat# sc- 9988 RRID:AB_626805 WB (1:1000) Antibody Anti-β-catenin (rabbit monoclonal) Cell Signaling Technology Cat# 8480 RRID:AB_11127855 WB (1:1000) Appendix 1 Continued on next page Filomena et al. eLife 2021;10:e58313. ..
Immunohistochemistry:Article Title: Functionally refined encoding of threat memory by distinct populations of basal forebrain cholinergic projection neurons.
Article Snippet: .. Appendix Page 25/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information strain, strain background (Mus musculus) Chat-IRES-Cre The Jackson Laboratory B6;129S6Chattm2(cre)Lowl/J stock number: 006410 strain, strain background (Mus musculus) Fos-tTA,FosshGFP The Jackson Laboratory TetTag stock number: 018306 strain, strain background (Escherichia coli) Stellar Competent Cells, HST08 Takara Cat#636766 genetic reagent (AAV9) AAV9-camk2aGCaMP6fWPRE-SV40 U. Penn Vector Core genetic reagent (AAV9) AAV9-DIO-eCFP This paper, Vector Biolabs Custom made genetic reagent (AAV9) AAV9-hSynGACh4.3 Vigene Biosciences Inc. genetic reagent (AAV8) AAV8-DIOhM4Di-mCherry Addgene Cat#44362 genetic reagent (AAV9) AAV9-TRE-DIOoChIEF-mCherryP2AtTAH100Y.SV40 This paper Cat#169414 Deposited to Addgene genetic reagent (AAV9) AAV9-TRE-DIOhM4Di-mCherry This paper Cat#169415 Deposited to Addgene genetic reagent (CAV2) CAV2-DIOhM4Di-mCherry Dr.EJ Kremer, Institut de Génétique Moléculaire de Montpellier, France. antibody anti-ChAT (Goat polyclonal) Millipore Cat# AB144P, RRID:AB_2079751 IHC (1:500) antibody anti-GFP (Rabbit polyclonal) Thermo Fisher Scienti c Cat#: A-11122; RRID:AB_221569 IHC (1:1000) Page 26/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information antibody anti-GFP (Rabbit polyclonal) Abcam Cat#: ab13970; RRID:AB_300798 IHC (1:500) antibody anti-mCherry (Mouse monoclonal) Takara Cat#: 632543; RRID:AB_2307319 IHC (1:500) antibody anti-DsRed (Rabbit polyclonal) Takara Cat#: 632496; RRID:AB_10013483 IHC (1:500) antibody anti-c-Fos (Rabbit polyclonal) Synaptic Systems Cat#: 226003; RRID:AB_2231974 IHC (1:500) antibody anti-Rabbit IgG (H + L)AlexaFluor 488 (Donkey polyclonal) Thermo Fisher Cat#: A32790; RRID:AB_2762833 IHC (1:1000) antibody anti-Rabbit IgG (H + L)Rhodamine RedX (Donkey polyclonal) Jackson Immunoresearch Cat#: 711-295-152; RRID:AB_2340613 IHC (1:1000) antibody anti-Goat IgG (H + L)- AlexaFluor 594(Donkey polyclonal) Thermo Fisher Cat#: A-11058; RRID:AB_142540 IHC (1:1000) antibody anti-Chicken IgY-Cy2 (Donkey polyclonal) Gift from Dr.Shaoyu Ge, Stony Brook University NY IHC (1:1000) chemical compound NeuroTraceTM 435/455 Blue Fluorescent Nissl Stain Thermo Fisher Cat#: N21479 IHC (1:500) recombinant DNA reagent pAAV-hSyn-DIOhM4D(Gi)mCherry (plasmid) Addgene Cat#44362 recombinant DNA reagent pV2SGE (plasmid) This paper Gift from Dr.Shaoyu Ge, Stony Brook University NY. .. Page 27/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information recombinant DNA reagent pAAV-TRE-DIOoChIEF-mCherryP2AtTAH100Y.SV40 (plasmid) This paper Deposited to Addgene Addgene Cat# 169414 recombinant DNA reagent pAAV-TRE-DIOhM4Di-mCherry (plasmid) This paper Deposited to Addgene Addgene Cat# 169415 sequencebased reagent chat_F IDT PCR primers TCTGGCAACTTCGTCGGA sequencedbased reagent chat_R IDT PCR primers CTCCTGGGCTGTTACGCAC sequencedbased reagent pV2.1 - Gene Block 7xTetO-LoxPLox2272tTAH100Y.SV40 IDT Gene block, custom sequencedbased reagent pV2.2- Gene Block oChIEF-LoxPLox2272 IDT Gene block, custom commercial assay or kit In-Fusion® HD Cloning Plus Takara/Clontech Cat#: 638920 commercial assay or kit High-Capacity cDNA Reverse Transcription Kit Applied Biosystems Cat#: 4368814 peptide, recombinant protein T4 DNA Ligase NEB Cat#M0202S peptide, recombinant protein BglII NEB Cat#R0144S peptide, recombinant protein AscI NEB Cat#R0558S peptide, recombinant protein BamHI-HF NEB Cat#R3136S Page 28/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information peptide, recombinant protein PmlI NEB Cat#R0532S peptide, recombinant protein Phusion® HighFidelity DNA Polymerase NEB Cat#M0530S chemical compound, drug Clozapine Sigma Aldrich Cat#C6305-25MG chemical compound, drug Fast Blue Polysciences Inc. Cat#17740-1 other Mt.Lion Pee Maine outdoor solutions LLC software, algorithm Prism GraphPad Software Inc. RRID:SCR_002798 software, algorithm Sigmaplot 12.5 Systat Software Inc. RRID:SCR_003210 software, algorithm OriginPro 9.1 Origin Lab Corporation RRID:SCR_014212 software, algorithm Fiji is just imagej Fiji RRID:SCR_002285 software, algorithm FreezeFrame v3 Actimetrics RRID:SCR_014429 software, algorithm MATLAB Mathworks RRID:SCR_001622 software, algorithm Pre-processing Analysis MATLAB Script for FiberPhotometry Doric software, algorithm ACh sensor analysis MATLAB script Crouse, Richard B., et al. Elife 9 (2020): e57335.
Staining:Article Title: Functionally refined encoding of threat memory by distinct populations of basal forebrain cholinergic projection neurons.
Article Snippet: .. Appendix Page 25/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information strain, strain background (Mus musculus) Chat-IRES-Cre The Jackson Laboratory B6;129S6Chattm2(cre)Lowl/J stock number: 006410 strain, strain background (Mus musculus) Fos-tTA,FosshGFP The Jackson Laboratory TetTag stock number: 018306 strain, strain background (Escherichia coli) Stellar Competent Cells, HST08 Takara Cat#636766 genetic reagent (AAV9) AAV9-camk2aGCaMP6fWPRE-SV40 U. Penn Vector Core genetic reagent (AAV9) AAV9-DIO-eCFP This paper, Vector Biolabs Custom made genetic reagent (AAV9) AAV9-hSynGACh4.3 Vigene Biosciences Inc. genetic reagent (AAV8) AAV8-DIOhM4Di-mCherry Addgene Cat#44362 genetic reagent (AAV9) AAV9-TRE-DIOoChIEF-mCherryP2AtTAH100Y.SV40 This paper Cat#169414 Deposited to Addgene genetic reagent (AAV9) AAV9-TRE-DIOhM4Di-mCherry This paper Cat#169415 Deposited to Addgene genetic reagent (CAV2) CAV2-DIOhM4Di-mCherry Dr.EJ Kremer, Institut de Génétique Moléculaire de Montpellier, France. antibody anti-ChAT (Goat polyclonal) Millipore Cat# AB144P, RRID:AB_2079751 IHC (1:500) antibody anti-GFP (Rabbit polyclonal) Thermo Fisher Scienti c Cat#: A-11122; RRID:AB_221569 IHC (1:1000) Page 26/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information antibody anti-GFP (Rabbit polyclonal) Abcam Cat#: ab13970; RRID:AB_300798 IHC (1:500) antibody anti-mCherry (Mouse monoclonal) Takara Cat#: 632543; RRID:AB_2307319 IHC (1:500) antibody anti-DsRed (Rabbit polyclonal) Takara Cat#: 632496; RRID:AB_10013483 IHC (1:500) antibody anti-c-Fos (Rabbit polyclonal) Synaptic Systems Cat#: 226003; RRID:AB_2231974 IHC (1:500) antibody anti-Rabbit IgG (H + L)AlexaFluor 488 (Donkey polyclonal) Thermo Fisher Cat#: A32790; RRID:AB_2762833 IHC (1:1000) antibody anti-Rabbit IgG (H + L)Rhodamine RedX (Donkey polyclonal) Jackson Immunoresearch Cat#: 711-295-152; RRID:AB_2340613 IHC (1:1000) antibody anti-Goat IgG (H + L)- AlexaFluor 594(Donkey polyclonal) Thermo Fisher Cat#: A-11058; RRID:AB_142540 IHC (1:1000) antibody anti-Chicken IgY-Cy2 (Donkey polyclonal) Gift from Dr.Shaoyu Ge, Stony Brook University NY IHC (1:1000) chemical compound NeuroTraceTM 435/455 Blue Fluorescent Nissl Stain Thermo Fisher Cat#: N21479 IHC (1:500) recombinant DNA reagent pAAV-hSyn-DIOhM4D(Gi)mCherry (plasmid) Addgene Cat#44362 recombinant DNA reagent pV2SGE (plasmid) This paper Gift from Dr.Shaoyu Ge, Stony Brook University NY. .. Page 27/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information recombinant DNA reagent pAAV-TRE-DIOoChIEF-mCherryP2AtTAH100Y.SV40 (plasmid) This paper Deposited to Addgene Addgene Cat# 169414 recombinant DNA reagent pAAV-TRE-DIOhM4Di-mCherry (plasmid) This paper Deposited to Addgene Addgene Cat# 169415 sequencebased reagent chat_F IDT PCR primers TCTGGCAACTTCGTCGGA sequencedbased reagent chat_R IDT PCR primers CTCCTGGGCTGTTACGCAC sequencedbased reagent pV2.1 - Gene Block 7xTetO-LoxPLox2272tTAH100Y.SV40 IDT Gene block, custom sequencedbased reagent pV2.2- Gene Block oChIEF-LoxPLox2272 IDT Gene block, custom commercial assay or kit In-Fusion® HD Cloning Plus Takara/Clontech Cat#: 638920 commercial assay or kit High-Capacity cDNA Reverse Transcription Kit Applied Biosystems Cat#: 4368814 peptide, recombinant protein T4 DNA Ligase NEB Cat#M0202S peptide, recombinant protein BglII NEB Cat#R0144S peptide, recombinant protein AscI NEB Cat#R0558S peptide, recombinant protein BamHI-HF NEB Cat#R3136S Page 28/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information peptide, recombinant protein PmlI NEB Cat#R0532S peptide, recombinant protein Phusion® HighFidelity DNA Polymerase NEB Cat#M0530S chemical compound, drug Clozapine Sigma Aldrich Cat#C6305-25MG chemical compound, drug Fast Blue Polysciences Inc. Cat#17740-1 other Mt.Lion Pee Maine outdoor solutions LLC software, algorithm Prism GraphPad Software Inc. RRID:SCR_002798 software, algorithm Sigmaplot 12.5 Systat Software Inc. RRID:SCR_003210 software, algorithm OriginPro 9.1 Origin Lab Corporation RRID:SCR_014212 software, algorithm Fiji is just imagej Fiji RRID:SCR_002285 software, algorithm FreezeFrame v3 Actimetrics RRID:SCR_014429 software, algorithm MATLAB Mathworks RRID:SCR_001622 software, algorithm Pre-processing Analysis MATLAB Script for FiberPhotometry Doric software, algorithm ACh sensor analysis MATLAB script Crouse, Richard B., et al. Elife 9 (2020): e57335.
Recombinant:Article Title: Functionally refined encoding of threat memory by distinct populations of basal forebrain cholinergic projection neurons.
Article Snippet: .. Appendix Page 25/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information strain, strain background (Mus musculus) Chat-IRES-Cre The Jackson Laboratory B6;129S6Chattm2(cre)Lowl/J stock number: 006410 strain, strain background (Mus musculus) Fos-tTA,FosshGFP The Jackson Laboratory TetTag stock number: 018306 strain, strain background (Escherichia coli) Stellar Competent Cells, HST08 Takara Cat#636766 genetic reagent (AAV9) AAV9-camk2aGCaMP6fWPRE-SV40 U. Penn Vector Core genetic reagent (AAV9) AAV9-DIO-eCFP This paper, Vector Biolabs Custom made genetic reagent (AAV9) AAV9-hSynGACh4.3 Vigene Biosciences Inc. genetic reagent (AAV8) AAV8-DIOhM4Di-mCherry Addgene Cat#44362 genetic reagent (AAV9) AAV9-TRE-DIOoChIEF-mCherryP2AtTAH100Y.SV40 This paper Cat#169414 Deposited to Addgene genetic reagent (AAV9) AAV9-TRE-DIOhM4Di-mCherry This paper Cat#169415 Deposited to Addgene genetic reagent (CAV2) CAV2-DIOhM4Di-mCherry Dr.EJ Kremer, Institut de Génétique Moléculaire de Montpellier, France. antibody anti-ChAT (Goat polyclonal) Millipore Cat# AB144P, RRID:AB_2079751 IHC (1:500) antibody anti-GFP (Rabbit polyclonal) Thermo Fisher Scienti c Cat#: A-11122; RRID:AB_221569 IHC (1:1000) Page 26/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information antibody anti-GFP (Rabbit polyclonal) Abcam Cat#: ab13970; RRID:AB_300798 IHC (1:500) antibody anti-mCherry (Mouse monoclonal) Takara Cat#: 632543; RRID:AB_2307319 IHC (1:500) antibody anti-DsRed (Rabbit polyclonal) Takara Cat#: 632496; RRID:AB_10013483 IHC (1:500) antibody anti-c-Fos (Rabbit polyclonal) Synaptic Systems Cat#: 226003; RRID:AB_2231974 IHC (1:500) antibody anti-Rabbit IgG (H + L)AlexaFluor 488 (Donkey polyclonal) Thermo Fisher Cat#: A32790; RRID:AB_2762833 IHC (1:1000) antibody anti-Rabbit IgG (H + L)Rhodamine RedX (Donkey polyclonal) Jackson Immunoresearch Cat#: 711-295-152; RRID:AB_2340613 IHC (1:1000) antibody anti-Goat IgG (H + L)- AlexaFluor 594(Donkey polyclonal) Thermo Fisher Cat#: A-11058; RRID:AB_142540 IHC (1:1000) antibody anti-Chicken IgY-Cy2 (Donkey polyclonal) Gift from Dr.Shaoyu Ge, Stony Brook University NY IHC (1:1000) chemical compound NeuroTraceTM 435/455 Blue Fluorescent Nissl Stain Thermo Fisher Cat#: N21479 IHC (1:500) recombinant DNA reagent pAAV-hSyn-DIOhM4D(Gi)mCherry (plasmid) Addgene Cat#44362 recombinant DNA reagent pV2SGE (plasmid) This paper Gift from Dr.Shaoyu Ge, Stony Brook University NY. .. Page 27/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information recombinant DNA reagent pAAV-TRE-DIOoChIEF-mCherryP2AtTAH100Y.SV40 (plasmid) This paper Deposited to Addgene Addgene Cat# 169414 recombinant DNA reagent pAAV-TRE-DIOhM4Di-mCherry (plasmid) This paper Deposited to Addgene Addgene Cat# 169415 sequencebased reagent chat_F IDT PCR primers TCTGGCAACTTCGTCGGA sequencedbased reagent chat_R IDT PCR primers CTCCTGGGCTGTTACGCAC sequencedbased reagent pV2.1 - Gene Block 7xTetO-LoxPLox2272tTAH100Y.SV40 IDT Gene block, custom sequencedbased reagent pV2.2- Gene Block oChIEF-LoxPLox2272 IDT Gene block, custom commercial assay or kit In-Fusion® HD Cloning Plus Takara/Clontech Cat#: 638920 commercial assay or kit High-Capacity cDNA Reverse Transcription Kit Applied Biosystems Cat#: 4368814 peptide, recombinant protein T4 DNA Ligase NEB Cat#M0202S peptide, recombinant protein BglII NEB Cat#R0144S peptide, recombinant protein AscI NEB Cat#R0558S peptide, recombinant protein BamHI-HF NEB Cat#R3136S Page 28/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information peptide, recombinant protein PmlI NEB Cat#R0532S peptide, recombinant protein Phusion® HighFidelity DNA Polymerase NEB Cat#M0530S chemical compound, drug Clozapine Sigma Aldrich Cat#C6305-25MG chemical compound, drug Fast Blue Polysciences Inc. Cat#17740-1 other Mt.Lion Pee Maine outdoor solutions LLC software, algorithm Prism GraphPad Software Inc. RRID:SCR_002798 software, algorithm Sigmaplot 12.5 Systat Software Inc. RRID:SCR_003210 software, algorithm OriginPro 9.1 Origin Lab Corporation RRID:SCR_014212 software, algorithm Fiji is just imagej Fiji RRID:SCR_002285 software, algorithm FreezeFrame v3 Actimetrics RRID:SCR_014429 software, algorithm MATLAB Mathworks RRID:SCR_001622 software, algorithm Pre-processing Analysis MATLAB Script for FiberPhotometry Doric software, algorithm ACh sensor analysis MATLAB script Crouse, Richard B., et al. Elife 9 (2020): e57335.
Article Title: Myofibril diameter is set by a finely tuned mechanism of protein oligomerization in Drosophila
Article Snippet: .. Recombinant DNA reagent Plasmid: pDESTpUAS-RfB-HACYFP-attB Sven Bogdan PMID: 20937809 FBrf0212496 Recombinant DNA reagent Plasmid: pDESTpUAS-RfB-mycNYFP-attB Sven Bogdan PMID: 20937809 FBrf0212496 Strain, strain background (Saccharomyces cerevisiae) Matchmaker Y2HGold Clontech 630498 Strain, strain background (E. coli) BL21 NEB C2530H Antibody Anti-Flag SIGMA F3165 1:200 Software, algorithm R Project for Statistical Computing: base and ape packages https://cran.r-project.org/ RRID:SCR_001905 Software, algorithm Salmon https://combinelab.github.io/salmon/ RRID:SCR_017036 Software, algorithm ImageJ/Fiji distribution https://fiji.sc/ RRID: SCR_002285 Software, algorithm Galaxy https://usegalaxy.org/ RRID:SCR_006281 Chemical compound, drug ethylene glycol bis-sulfosuccinimidyl succinate (EGS) Fisher Scientific 21565 Chemical compound, drug YPDA medium Clontech 630464 Chemical compound, drug Minimal SD Base Clontech 630411 Chemical compound, drug -Leu /- Trp DO Supplement Clontech 630417 Chemical compound, drug -Ade /- His /- Leu/-Trp DO Supplement Clontech 630428 Chemical compound, drug Acti-stain 488 phalloidin CYTOSKELETON, INC PHDG1-A Continued on next page González-Morales et al. eLife 2019;8:e50496. .. DOI: https://doi.org/10.7554/eLife.50496 16 of 23 Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug Alexa633Phalloidin Fisher Scientific A22284 Chemical compound, drug Rhodaminephalloidin Fisher Scientific 10063052
Plasmid Preparation:Article Title: Functionally refined encoding of threat memory by distinct populations of basal forebrain cholinergic projection neurons.
Article Snippet: .. Appendix Page 25/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information strain, strain background (Mus musculus) Chat-IRES-Cre The Jackson Laboratory B6;129S6Chattm2(cre)Lowl/J stock number: 006410 strain, strain background (Mus musculus) Fos-tTA,FosshGFP The Jackson Laboratory TetTag stock number: 018306 strain, strain background (Escherichia coli) Stellar Competent Cells, HST08 Takara Cat#636766 genetic reagent (AAV9) AAV9-camk2aGCaMP6fWPRE-SV40 U. Penn Vector Core genetic reagent (AAV9) AAV9-DIO-eCFP This paper, Vector Biolabs Custom made genetic reagent (AAV9) AAV9-hSynGACh4.3 Vigene Biosciences Inc. genetic reagent (AAV8) AAV8-DIOhM4Di-mCherry Addgene Cat#44362 genetic reagent (AAV9) AAV9-TRE-DIOoChIEF-mCherryP2AtTAH100Y.SV40 This paper Cat#169414 Deposited to Addgene genetic reagent (AAV9) AAV9-TRE-DIOhM4Di-mCherry This paper Cat#169415 Deposited to Addgene genetic reagent (CAV2) CAV2-DIOhM4Di-mCherry Dr.EJ Kremer, Institut de Génétique Moléculaire de Montpellier, France. antibody anti-ChAT (Goat polyclonal) Millipore Cat# AB144P, RRID:AB_2079751 IHC (1:500) antibody anti-GFP (Rabbit polyclonal) Thermo Fisher Scienti c Cat#: A-11122; RRID:AB_221569 IHC (1:1000) Page 26/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information antibody anti-GFP (Rabbit polyclonal) Abcam Cat#: ab13970; RRID:AB_300798 IHC (1:500) antibody anti-mCherry (Mouse monoclonal) Takara Cat#: 632543; RRID:AB_2307319 IHC (1:500) antibody anti-DsRed (Rabbit polyclonal) Takara Cat#: 632496; RRID:AB_10013483 IHC (1:500) antibody anti-c-Fos (Rabbit polyclonal) Synaptic Systems Cat#: 226003; RRID:AB_2231974 IHC (1:500) antibody anti-Rabbit IgG (H + L)AlexaFluor 488 (Donkey polyclonal) Thermo Fisher Cat#: A32790; RRID:AB_2762833 IHC (1:1000) antibody anti-Rabbit IgG (H + L)Rhodamine RedX (Donkey polyclonal) Jackson Immunoresearch Cat#: 711-295-152; RRID:AB_2340613 IHC (1:1000) antibody anti-Goat IgG (H + L)- AlexaFluor 594(Donkey polyclonal) Thermo Fisher Cat#: A-11058; RRID:AB_142540 IHC (1:1000) antibody anti-Chicken IgY-Cy2 (Donkey polyclonal) Gift from Dr.Shaoyu Ge, Stony Brook University NY IHC (1:1000) chemical compound NeuroTraceTM 435/455 Blue Fluorescent Nissl Stain Thermo Fisher Cat#: N21479 IHC (1:500) recombinant DNA reagent pAAV-hSyn-DIOhM4D(Gi)mCherry (plasmid) Addgene Cat#44362 recombinant DNA reagent pV2SGE (plasmid) This paper Gift from Dr.Shaoyu Ge, Stony Brook University NY. .. Page 27/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information recombinant DNA reagent pAAV-TRE-DIOoChIEF-mCherryP2AtTAH100Y.SV40 (plasmid) This paper Deposited to Addgene Addgene Cat# 169414 recombinant DNA reagent pAAV-TRE-DIOhM4Di-mCherry (plasmid) This paper Deposited to Addgene Addgene Cat# 169415 sequencebased reagent chat_F IDT PCR primers TCTGGCAACTTCGTCGGA sequencedbased reagent chat_R IDT PCR primers CTCCTGGGCTGTTACGCAC sequencedbased reagent pV2.1 - Gene Block 7xTetO-LoxPLox2272tTAH100Y.SV40 IDT Gene block, custom sequencedbased reagent pV2.2- Gene Block oChIEF-LoxPLox2272 IDT Gene block, custom commercial assay or kit In-Fusion® HD Cloning Plus Takara/Clontech Cat#: 638920 commercial assay or kit High-Capacity cDNA Reverse Transcription Kit Applied Biosystems Cat#: 4368814 peptide, recombinant protein T4 DNA Ligase NEB Cat#M0202S peptide, recombinant protein BglII NEB Cat#R0144S peptide, recombinant protein AscI NEB Cat#R0558S peptide, recombinant protein BamHI-HF NEB Cat#R3136S Page 28/44 Key Resources Table Reagent type (species) or resource Designation Source or reference Identi ers Additional information peptide, recombinant protein PmlI NEB Cat#R0532S peptide, recombinant protein Phusion® HighFidelity DNA Polymerase NEB Cat#M0530S chemical compound, drug Clozapine Sigma Aldrich Cat#C6305-25MG chemical compound, drug Fast Blue Polysciences Inc. Cat#17740-1 other Mt.Lion Pee Maine outdoor solutions LLC software, algorithm Prism GraphPad Software Inc. RRID:SCR_002798 software, algorithm Sigmaplot 12.5 Systat Software Inc. RRID:SCR_003210 software, algorithm OriginPro 9.1 Origin Lab Corporation RRID:SCR_014212 software, algorithm Fiji is just imagej Fiji RRID:SCR_002285 software, algorithm FreezeFrame v3 Actimetrics RRID:SCR_014429 software, algorithm MATLAB Mathworks RRID:SCR_001622 software, algorithm Pre-processing Analysis MATLAB Script for FiberPhotometry Doric software, algorithm ACh sensor analysis MATLAB script Crouse, Richard B., et al. Elife 9 (2020): e57335.
Article Title: Myofibril diameter is set by a finely tuned mechanism of protein oligomerization in Drosophila
Article Snippet: .. Recombinant DNA reagent Plasmid: pDESTpUAS-RfB-HACYFP-attB Sven Bogdan PMID: 20937809 FBrf0212496 Recombinant DNA reagent Plasmid: pDESTpUAS-RfB-mycNYFP-attB Sven Bogdan PMID: 20937809 FBrf0212496 Strain, strain background (Saccharomyces cerevisiae) Matchmaker Y2HGold Clontech 630498 Strain, strain background (E. coli) BL21 NEB C2530H Antibody Anti-Flag SIGMA F3165 1:200 Software, algorithm R Project for Statistical Computing: base and ape packages https://cran.r-project.org/ RRID:SCR_001905 Software, algorithm Salmon https://combinelab.github.io/salmon/ RRID:SCR_017036 Software, algorithm ImageJ/Fiji distribution https://fiji.sc/ RRID: SCR_002285 Software, algorithm Galaxy https://usegalaxy.org/ RRID:SCR_006281 Chemical compound, drug ethylene glycol bis-sulfosuccinimidyl succinate (EGS) Fisher Scientific 21565 Chemical compound, drug YPDA medium Clontech 630464 Chemical compound, drug Minimal SD Base Clontech 630411 Chemical compound, drug -Leu /- Trp DO Supplement Clontech 630417 Chemical compound, drug -Ade /- His /- Leu/-Trp DO Supplement Clontech 630428 Chemical compound, drug Acti-stain 488 phalloidin CYTOSKELETON, INC PHDG1-A Continued on next page González-Morales et al. eLife 2019;8:e50496. .. DOI: https://doi.org/10.7554/eLife.50496 16 of 23 Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug Alexa633Phalloidin Fisher Scientific A22284 Chemical compound, drug Rhodaminephalloidin Fisher Scientific 10063052
other:Article Title: FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy
Article Snippet: DOI: https://doi.org/10.7554/eLife.47327 20 of 34 Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug Halt Protease Inhibitor Cocktail (100X) Thermo Fischer Scientific Cat# 87786 Chemical compound, drug staurosporine Cell Signaling Technology Cat# 9953S Chemical compound, drug cisplatin Enzo Life Sciences Cat# 89150–634 Chemical compound, drug GSK inhibitor CHIR99021 Millipore Sigma Cat# SML1046 Chemical compound, drug Propidium iodide BioLegend Cat# 421301 Chemical compound, drug DTT Bio Basic Cat# DB0058-5 Peptide, recombinant protein Mouse FAK (phospho Y397) peptide Abcam Cat# ab40145 Commercial assay, kit PureLink RNA Mini Kit Thermo Fisher Scientific Cat# 12183020 Commercial assay, kit Ambion Homogenizer Thermo Fisher Scientific Cat# 12183026 Commercial assay, kit XTT Cell Proliferation Assay Kit ATCC Cat# 30–1011K Commercial assay, kit Dual-Luciferase Reporter Assay System Promega Cat# E1910 Commercial assay, kit PE Annexin V Apoptosis Detection Kit I BD Biosciences Cat# 559763 Commercial assay, kit AlamarBlue Cell Viability Reagent Thermo Fischer Scientific Cat# DAL1025 Commercial assay, kit iTaq Universal SYBR Green Supermix Biorad Cat# 1725121 Commercial assay, kit High-Capacity cDNA Reverse Transcription Kit Thermo Fisher Scientific Cat# 4368814 Commercial assay, kit AldeRed ALDH Detection Assay Millipore Sigma Cat# SCR150 Cell line (Homo-sapiens) OVCAR3 NCI Tumor Repository RRID:CVCL_0465 Cell line (Homo-sapiens) OVCAR10 Denise Connolly (Fox Chase Cancer Center) RRID:CVCL_4377 Cell line (Homo-sapiens) OVCAR10-CP this paper Schlaepfer Lab Cell line (Homo-sapiens) A2780 Denise Connolly (Fox Chase Cancer Center) RRID:CVCL_0134 Cell line (Homo-sapiens) A2780-CP70 Denise Connolly (Fox Chase Cancer Center) RRID:CVCL_0135 Cell line (Mus-musculus) ID8 Katherine Roby (University of Kansas Medical Center) RRID:CVCL_IU14 Continued on next page Diaz Osterman et al. eLife 2019;8:e47327.
Article Title: CHD-associated enhancers shape human cardiomyocyte lineage commitment
Article Snippet: DOI: https://doi.org/10.7554/eLife.86206 16 of 27 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug CHIR99021 Tocris Cat#4423 Chemical compound, drug Wnt- C59 Cayman Cat#16644 Chemical compound, drug Accutase Sigma- Aldrich Cat#SCR005 Chemical compound, drug Insulin Gibco Cat#12585014 Chemical compound, drug B- 27 Thermo Fisher Cat#17504044 Chemical compound, drug Molecular Probes Fura- 2 Thermo Fisher Cat#F1221 Chemical compound, drug Pluronic F- 127 Thermo Fisher Cat#P6867 Antibody Anti- human- FN1 (Rabbit polyclonal) Thermo Fisher Cat#PA5- 29578 WB(1:1000) Antibody Anti- rabbit IgG Cell Signaling Technology CST #7074 WB(1:400) Chemical compound, drug KAPA HiFi HS KAPA Cat#KK2502 Commercial assay, kit PrimeFlow RNA Assay Kit Thermo Fisher Cat#88- 18005- 210 Chemical compound, drug NEBNext High- Fidelity New England Biolabs Cat#M0541L Chemical compound, drug Gibson Assembly Master Mix New England Biolabs Cat#E2611L Chemical compound, drug mTeSR Plus Stemcell Technologies Cat#100–0276 Chemical compound, drug Matrigel Corning Cat#354277 Commercial assay, kit P3 Primary Cell 4DNucleofector X Kit Lonza Cat#V4XP- 3024 Commercial assay, kit 10× genomics Chromium Single Cell 3′ Kit V3.1 10× Genomics Cat#PN- 1000147 Commercial assay, kit 10× CellPlex 10× Genomics Cat#PN- 1000261 Commercial assay, kit 10× Target Hybridization Kit 10× Genomics Cat#PN- 1000248 Chemical compound, drug RPMI 1640 Thermo Fisher Cat#11875093 Chemical compound, drug KnockOut Serum Thermo Fisher Cat#10828028 Chemical compound, drug HHBSS Corning Cat#21- 023- CM Strain, strain background (Endura) Endura ElectroCompetent Cells Lucigen Cat#60242–2 Electrocompetent Cells Strain, strain background (Escherichia coli) Stellar Competent Cells Clontech Cat#636766 Other Single- cell RNA- seq Data This paper GEO: GSE190475 Sequencing data located at GEO Continued Continued on next page Armendariz, Goetsch et al. eLife 2023;12:e86206.
Y2H Assay:Article Title: A conserved mycobacterial nucleomodulin hijacks the host COMPASS complex to reprogram pro-inflammatory transcription and promote intracellular survival
Article Snippet: Strain, strain background ( Escherichia coli ) , E. coli DH5a , , ATCC: Cat#25922 , . .. Strain, strain background (Y2HGold Chemically Competent Cell) , Y2HGold , Clontech , Cat#630498 , GAL4-based yeast strain for two-hybrid assays; see ‘Materials and methods: Y2H assay’ for details.. .. Cell line ( Homo sapiens ) , HEK293T , Cellosaurus , Cat#CRL-3216 RRID: CVCL_0063 , Authenticated and mycoplasma-free; see ‘Materials and methods: Cell culture’ for details..
Western Blot:Article Title: Myopalladin knockout mice develop cardiac dilation and show a maladaptive response to mechanical pressure overload
Article Snippet: .. (species) or resource Designation Source or reference Identifiers Additional information Strain, strain background (male Mus musculus) MYPN knockout (MKO) mice (in C57BL/6 J background) Filomena et al., 2020 N/A Strain, strain background (Mus musculus) C57BL/6 J The Jackson Laboratories Cat# 000664 RRID:IMSR_ JAX:000664 Strain, strain background (Escherichia coli) DH5α electrocompetent cells New England BioLabs Cat# C2989K Strain, strain background (Escherichia coli) BL21- CodonPlus (DE3)RIPL strain Agilent Technologies Cat# 230280 Strain, strain background (Saccharomyces cerevisiae) Y2H Gold yeast strain Takara Bio Cat# 630498 Strain, strain background (Saccharomyces cerevisiae) L40 yeast strain Takara Bio N/A Antibody Anti- MYPN (rabbit polyclonal) Yamamoto et al., 2013 N/A WB (1:1000) Antibody Anti- PALLD 621 (rabbit polyclonal) Pogue- Geile et al., 2006 Kindly provided by Prof. Carol Otey, University of North Carolina, Chapel Hill, NC, USA WB (1:500) IF (1:30) Antibody Anti- NEBL (rabbit polyclonal) Mastrototaro et al., 2015 N/A WB (1:500) Antibody Anti- ANKRD1/CARP (rabbit polyclonal) Miller et al., 2003 N/A WB (1:200) IF (1:20) Antibody Anti- Cypher (rabbit polyclonal) Zhou et al., 2001 Kindly provided by Prof. Ju Chen, University of California San Diego, La Jolla, CA, USA WB (1:500) IF (1:50) Antibody Anti-α-actinin (mouse monoclonal) Merck Life Science Cat# A7811 RRID:AB_476766 WB (1:50000) IF (1:250) Antibody Anti- desmin (rabbit polyclonal) Abcam Cat# Ab8592 RRID:AB_306653 IF (1:80) Antibody Anti- MKL1/MRTF- A (rabbit polyclonal) Merck Life Science Cat# AV37504 RRID:AB_1853972 IF (1:30) Antibody Anti- MKL1/MRTF- A (rabbit polyclonal) Immunological Sciences Cat# AB- 84312 RRID:AB_2892156 WB (1:500) Antibody Anti- desmoplakin 1/2 (mouse monoclonal) Bio- Rad Laboratories Cat# 2722–5204 RRID:AB_619950 WB (1:750) Antibody Anti-α-E- catenin (mouse monoclonal) Santa Cruz Biotechnology Cat# sc- 9988 RRID:AB_626805 WB (1:1000) Antibody Anti-β-catenin (rabbit monoclonal) Cell Signaling Technology Cat# 8480 RRID:AB_11127855 WB (1:1000) Appendix 1 Continued on next page Filomena et al. eLife 2021;10:e58313. ..
Software:Article Title: Myofibril diameter is set by a finely tuned mechanism of protein oligomerization in Drosophila
Article Snippet: .. Recombinant DNA reagent Plasmid: pDESTpUAS-RfB-HACYFP-attB Sven Bogdan PMID: 20937809 FBrf0212496 Recombinant DNA reagent Plasmid: pDESTpUAS-RfB-mycNYFP-attB Sven Bogdan PMID: 20937809 FBrf0212496 Strain, strain background (Saccharomyces cerevisiae) Matchmaker Y2HGold Clontech 630498 Strain, strain background (E. coli) BL21 NEB C2530H Antibody Anti-Flag SIGMA F3165 1:200 Software, algorithm R Project for Statistical Computing: base and ape packages https://cran.r-project.org/ RRID:SCR_001905 Software, algorithm Salmon https://combinelab.github.io/salmon/ RRID:SCR_017036 Software, algorithm ImageJ/Fiji distribution https://fiji.sc/ RRID: SCR_002285 Software, algorithm Galaxy https://usegalaxy.org/ RRID:SCR_006281 Chemical compound, drug ethylene glycol bis-sulfosuccinimidyl succinate (EGS) Fisher Scientific 21565 Chemical compound, drug YPDA medium Clontech 630464 Chemical compound, drug Minimal SD Base Clontech 630411 Chemical compound, drug -Leu /- Trp DO Supplement Clontech 630417 Chemical compound, drug -Ade /- His /- Leu/-Trp DO Supplement Clontech 630428 Chemical compound, drug Acti-stain 488 phalloidin CYTOSKELETON, INC PHDG1-A Continued on next page González-Morales et al. eLife 2019;8:e50496. .. DOI: https://doi.org/10.7554/eLife.50496 16 of 23 Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug Alexa633Phalloidin Fisher Scientific A22284 Chemical compound, drug Rhodaminephalloidin Fisher Scientific 10063052
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