Plasmid Preparation:Article Title: Mechanism-Based Personalized Medicine for Cystic Fibrosis by Suppressing Pseudo Exon Inclusion.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER pSS21_ CFTRWT-GFP (CFTR CDS+truncated IVS22 (WT) with N-terminal mKate2-GP2A and C-terminal HiBiTHA-AcGFP) This paper N/A pSS22_ CFTRC>T-GFP (CFTR CDS+truncated IVS22 (3849+10kb C>T) with N-terminal mKate2-GP2A and C-terminal HiBiT-HA-AcGFP) This paper N/A pSS23_ CFTRF508d-GFP (CFTR CDS (DF508 ) with N-terminal mKate2-GP2A and C-terminal AcGFP) This paper N/A CFTR WT_HiBiT Promega N/A (Gift from Promega) CFTR_delF508_HiBiT Promega N/A (Gift from Promega) pME-mKate2 no stop vector Fowler et al., 2016 Addgene plasmid # 80806 (pME-mKate2 no stop) pcDNA3.1 EYFP H148Q/I152L Galietta et al., 2001 Addgene plasmid # 25872 (pcDNA3.1 EYFP H148Q/I152L) Software and Algorithms GraphPad Prism Version 8 GraphPad Software, San Diego, CA, USA www.graphpad.com Hybrid cell count BZ-H3C software Keyence, Osaka, Japan https://www.keyence.com/ Image Lab software Bio-Rad Laboratories, Inc., Hercules, CA, USA https://www.bio-rad.com/ Cell Chemical Biology 27, 1–11.e1–e6, December 17, 2020 e2 system, the normal-type splicing (skipping of the pseudo exon) leads to the expression of a GFP-fusion protein. ..
Article Title: Different translation dynamics of β- and γ-actin regulates cell migration
Article Snippet: .. Recombinant DNA reagent pUbC-FLAG-24xSuntagV4oxEBFP-AID-baUTR124xMS2V5-Wpre (plasmid) Wu et al., 2016 Addgene plasmid # 84561 Plasmid containing Suntag, AID, b-actin 30UTR, MS2 repeats. ..
Article Title: Different translation dynamics of β- and γ-actin regulates cell migration
Article Snippet: .. Recombinant DNA reagent UbC NLS HA stdMCP stdHalo Voigt et al., 2017 Addgene plasmid # 104999 Plasmid containing MCP tandem dimer fused to HaloTag tandem dimer to visualize MS2 repeat containing RNA Recombinant DNA reagent pUbC-nls-hastdMCP-stdGFP Wu et al., 2016 Addgene plasmid # 98916 Plasmid containing MCP tandem dimer fused to GFP tandem dimer. ..
Article Title: TEMPO enables sequential genetic labeling and manipulation of vertebrate cell lineages.
Article Snippet: .. GCACATGTCG This manuscript PB-REV Recombinant DNA p5E-ubi Mosimann et al., 2011 Addgene Plasmid #27320; RRID: Addgene_27320 pDestTol2pA2 Kwan et al., 2007 #394 pME-MCS Kwan et al., 2007 #237 p3E-MCS Don et al., 2017 Addgene Plasmid #75174; RRID: Addgene_75174 ZebraF-Cassa-#3 Garcia-Marques et al., 2019 ZebraF-Cassa-#3 pME-H2B-mCerulean3 Don et al., 2017 Addgene plasmid #75156; RRID: Addgene_75156 pToneDest (pDesTol1) Shin et al., 2016 Addgene plasmid #67691; RRID: Addgene_67691 p5E-5xUAS vector Asakawa et al., 2008 p5E-5xUAS pME-zCas9 Ablain et al., 2015 Addgene plasmid # 63154; RRID: Addgene_63154 p5E-her4.1 Yeo et al., 2007 p5E-her4.1 pXL-CMV-piggyBac Transposagen Biopharmaceuticals Inc N/A pcDNA3.1/Puro-CAG-ASAP1 St-Pierre et al., 2014 Addgene plasmid # 52519; RRID: Addgene_52519 PB-CA-pDest Woltjen et al., 2009 Addgene plasmid # 20960; RRID: Addgene_20960 pX330-U6-Chimeric_BB-CBh-hSpCas9 Cong et al., 2013 Addgene plasmid # 42230; RRID: Addgene_42230 pCS2-Tol1.zf1 Horstick et al., 2015 Addgene plasmid # 61388; RRID: Addgene_61388 pCS2FA-transposase Clark et al., 2011 Tolkit plasmid #396 ubi:TEMPO-gRNA1_Tol1 This manuscript zTEMPO_1 ubi:TEMPO_Tol1 This manuscript zTEMPO_2 ubi:TEMPO-RFPon-gRNA2_Tol1 This manuscript zTEMPO_3 ubi:TEMPO-RFPon _Tol1 This manuscript zTEMPO_4 (Continued on next page) ll OPEN ACCESSNeuroResource Neuron 111, 345–361.e1–e10, February 1, 2023 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER ubi:TEMPO-RFPon-gRNA2switchgRNA1_Tol1 This manuscript zTEMPO_5 ubi:TEMPO-RFPon-gRNA2switch _Tol1 This manuscript zTEMPO_6 UAS:TEMPO-gRNA1_Tol1 This manuscript zTEMPO_7 TRE:TEMPO-gRNA1_Tol2 This manuscript zTEMPO_8 ubi:4-step-TEMPO-gRNA1_Tol2 This manuscript zTEMPO_9 ubi:4-step-TEMPO_Tol2 This manuscript zTEMPO_10 ubi:Cas9-H2B-Halotag-gRNA2switch_Tol1 This manuscript zTEMPO_11 ubi:Cas9-H2B-Halotag_gRNA3switch_Tol1 This manuscript zTEMPO_12 ubi:Cas9-H2B-Halotag_Tol1 This manuscript zTEMPO_13 ubi:Cas9gRNA3switch_gRNA2switch_Tol2 This manuscript zTEMPO_14 her4.1:Cas9-H2B-HalotaggRNA2switch_Tol1 This manuscript zTEMPO_15 TRE:Cas9-H2B-HalotaggRNA2switch_Tol1 This manuscript zTEMPO_16 ubi:Gal4-gRNA2switch_Tol2 This manuscript zTEMPO_17 her4.1:tTA_Tol2 This manuscript zTEMPO_18 pCS2-Gal4ff.zf1 Horstick et al., 2015 Addgene plasmid # 61392; RRID: Addgene_61392 pTet-Off Advanced Vector Takara Cat#631070 CAG-PB This manuscript #406 CAG:TEMPO-gRNA1_PB This manuscript mTEMPO_1 CAG:4-step-TEMPO-gRNA1_PB This manuscript mTEMPO_2 CAG:TEMPO-T1CD1-gRNA1_PB This manuscript mTEMPO_3 CAG:TEMPO-T2CD1-gRNA1_PB This manuscript mTEMPO_4 CAG:TEMPO-T3CD1-gRNA1_PB This manuscript mTEMPO_5 CAG:TEMPO-AllFramesCD1-gRNA1_PB This manuscript mTEMPO_6 CAG:TEMPO-T1CB1-gRNA1_PB This manuscript mTEMPO_7 CAG:TEMPO-T2CB1-gRNA1_PB This manuscript mTEMPO_8 CAG:Cas9-H2BHalotag_gRNA2switch_PB This manuscript mTEMPO_9 gRNAswitch3_CAG:Cas9_ gRNA2switch_PB This manuscript mTEMPO_10 Episomal CAG-Halotag This manuscript mTEMPO_11 Software and algorithms Fiji (ImageJ version 2.0.0-rc-68/1.52e) NIH RRID: SCR_002285 Benchling Benchling platform RRID: SCR_013955 Adobe Illustrator CC 2018 Adobe RRID: SCR_010279 Other cell culture insert Millipore PICM0RG50 ll OPEN ACCESS NeuroResource
Article Title: iPSC modeling of stage-specific leukemogenesis reveals BAALC as a key oncogene in severe congenital neutropenia.
Article Snippet: 2013 Addgene Plasmid # 48138 pCMV-BE3 Komor A et al., Nature. .. 2016 Addgene Plasmid #73021 BAALC_p.19.NLS.BE3.2xNLS.GFP.PX458 This paper N/A Software and algorithms GraphPad Prism 8 GraphPad Software Inc. https://www.graphpad.com/ FlowJo V10 BD https://www.flowjo.com/ QuantStudio 3D Digital PCR Analysis Suite Software Thermo Fisher https://www.thermofisher.com/us/en/home/ life-science/pcr/digital-pcr/quantstudio-3ddigital-pcr-system/quantstudio-3d-software.html Connectivity map (CMAP) CLUE platform https://clue.io/cmap Feature Extraction Software Agilent Technologies https://www.agilent.com/en/product/mirna- microarray-platform/mirna-microarraysoftware/feature-extraction-software-228496 Agilent Genomic-Workbench Agilent Technologies https://www.agilent.com/en/product/cgh- cgh-snp-microarray-platform/cgh-cgh-snpmicroarray-software/agilent-genomicworkbench-228497 CRISPOR Concordet J et al., Nucleic Acid Research. ..
Article Title: A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-H3K27ac Abcam Cat# ab4729, RRID: AB_2118291 Mouse monoclonal anti-CD24 APC-eFluor 780 Thermo Fisher Scientific Cat# 47-0242-82, RRID: AB_10853172 Chicken polyclonal anti-GFP Thermo Fisher Scientific Cat# A10262, RRID: AB_2534023 Rabbit polyclonal anti-RFP Abcam Cat# ab62341, RRID: AB_945213 Rabbit polyclonal anti-Tet1 GeneTex Cat# GTX125888, RRID:AB_11164485 Mouse polyclonal anti-Dnmt3a Novus Biological Cat# NB120-13888, RRID: AB_789607 Mouse anti-Isl1/2 Jessell Lab/HHMI CU RRID: AB_2314683 Chemicals, peptides, and recombinant proteins Lipofectamine 2000 Invitrogen Cat# 11668019 T7 endonuclease NEB Cat# M0302L Protein G Dynabeads Invitrogen Cat# 10004D Ampure XP beads Beckman Coulter Cat# A63880 Di(N-succinimidyl) glutarate (DSG) Sigma Cat# 80424 Retinoic acid Sigma Cat# R2625 Deposited data Raw and analyzed allele-specific 4C-seq data This paper GSE148315 Mouse reference genome GRCm38 (mm10) Genome Reference Consortium https://www.ncbi.nlm.nih.gov/assembly/ GCF_000001635.20/ Experimental models: Cell lines Mouse B6J: iPSC Dlk1matVenus/patTomato, clone #6aa Swanzey and Stadtfeld, 2016 N/A Mouse matJF1/patB6N/J: iPSC Dlk1matTomato/patVenus, clone #104 This paper N/A Dnmt3ab KO ESCs, clone DKO#9 Lei et al., 1996 N/A Tet1/2/3 KO ESCs, clone TKO#9 Dawlaty et al., 2014 N/A Tet1/2/3 WT ESCs, clone WT#8 Dawlaty et al., 2014 N/A Oligonucleotides See Table S1 gRNAs and primer sequences N/A N/A Recombinant DNA pdCas9-Dnmt3a-puro Vojta et al., 2016 Addgene Plasmid #71667 pPGKENTRY-dCas9-Tet1CD Verma et al., 2018 N/A pMIGR1-IRES-BSD This paper N/A pBS-Dlk1-tomato Swanzey and Stadtfeld, 2016 N/A pHR-SFFV-dCAS9-BFP-KRAB Gilbert et al., 2013 Addgene Plasmid #46911 pLKO5.sgRNA.EFS.PAC Heckl et al., 2014 Addgene Plasmid #57825 pSpCas9(BB)-2A-GFP (pX458) Ran et al., 2013 Addgene Plasmid #48138 pHR-EF1a-dCAS9-Dnmt3a-BSD This paper N/A pHR-EF1a-dCAS9-Tet1-BSD This paper N/A pLKO5.sgRNA.EFS.PAC - F+E - Neo This paper N/A pHR-EF1a-dCAS9-BFP-KRAB This paper N/A pX330-PGK-NeoR Cong et al., 2013 Addgene Plasmid #42230 (Continued on next page) e1 Developmental Cell 56, 3052–3065.e1–e5, November 22, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms FlowJo (v10.7.0) BD Biosciences http://v9docs.flowjo.com/html/index.html RRID: SCR_008520 IGV browser Robinson et al., 2011 https://software.broadinstitute.org/ software/igv/ RRID:SCR_011793 Samtools (v1.8) Li et al., 2009 http://samtools.sourceforge.net/ RRID:SCR_002105 ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ RRID:SCR_003070 GraphPad Prism GraphPad http://www.graphpad.com/ RRID:SCR_002798
Software:Article Title: Mechanism-Based Personalized Medicine for Cystic Fibrosis by Suppressing Pseudo Exon Inclusion.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER pSS21_ CFTRWT-GFP (CFTR CDS+truncated IVS22 (WT) with N-terminal mKate2-GP2A and C-terminal HiBiTHA-AcGFP) This paper N/A pSS22_ CFTRC>T-GFP (CFTR CDS+truncated IVS22 (3849+10kb C>T) with N-terminal mKate2-GP2A and C-terminal HiBiT-HA-AcGFP) This paper N/A pSS23_ CFTRF508d-GFP (CFTR CDS (DF508 ) with N-terminal mKate2-GP2A and C-terminal AcGFP) This paper N/A CFTR WT_HiBiT Promega N/A (Gift from Promega) CFTR_delF508_HiBiT Promega N/A (Gift from Promega) pME-mKate2 no stop vector Fowler et al., 2016 Addgene plasmid # 80806 (pME-mKate2 no stop) pcDNA3.1 EYFP H148Q/I152L Galietta et al., 2001 Addgene plasmid # 25872 (pcDNA3.1 EYFP H148Q/I152L) Software and Algorithms GraphPad Prism Version 8 GraphPad Software, San Diego, CA, USA www.graphpad.com Hybrid cell count BZ-H3C software Keyence, Osaka, Japan https://www.keyence.com/ Image Lab software Bio-Rad Laboratories, Inc., Hercules, CA, USA https://www.bio-rad.com/ Cell Chemical Biology 27, 1–11.e1–e6, December 17, 2020 e2 system, the normal-type splicing (skipping of the pseudo exon) leads to the expression of a GFP-fusion protein. ..
Article Title: iPSC modeling of stage-specific leukemogenesis reveals BAALC as a key oncogene in severe congenital neutropenia.
Article Snippet: 2013 Addgene Plasmid # 48138 pCMV-BE3 Komor A et al., Nature. .. 2016 Addgene Plasmid #73021 BAALC_p.19.NLS.BE3.2xNLS.GFP.PX458 This paper N/A Software and algorithms GraphPad Prism 8 GraphPad Software Inc. https://www.graphpad.com/ FlowJo V10 BD https://www.flowjo.com/ QuantStudio 3D Digital PCR Analysis Suite Software Thermo Fisher https://www.thermofisher.com/us/en/home/ life-science/pcr/digital-pcr/quantstudio-3ddigital-pcr-system/quantstudio-3d-software.html Connectivity map (CMAP) CLUE platform https://clue.io/cmap Feature Extraction Software Agilent Technologies https://www.agilent.com/en/product/mirna- microarray-platform/mirna-microarraysoftware/feature-extraction-software-228496 Agilent Genomic-Workbench Agilent Technologies https://www.agilent.com/en/product/cgh- cgh-snp-microarray-platform/cgh-cgh-snpmicroarray-software/agilent-genomicworkbench-228497 CRISPOR Concordet J et al., Nucleic Acid Research. ..
Cell Characterization:Article Title: Mechanism-Based Personalized Medicine for Cystic Fibrosis by Suppressing Pseudo Exon Inclusion.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER pSS21_ CFTRWT-GFP (CFTR CDS+truncated IVS22 (WT) with N-terminal mKate2-GP2A and C-terminal HiBiTHA-AcGFP) This paper N/A pSS22_ CFTRC>T-GFP (CFTR CDS+truncated IVS22 (3849+10kb C>T) with N-terminal mKate2-GP2A and C-terminal HiBiT-HA-AcGFP) This paper N/A pSS23_ CFTRF508d-GFP (CFTR CDS (DF508 ) with N-terminal mKate2-GP2A and C-terminal AcGFP) This paper N/A CFTR WT_HiBiT Promega N/A (Gift from Promega) CFTR_delF508_HiBiT Promega N/A (Gift from Promega) pME-mKate2 no stop vector Fowler et al., 2016 Addgene plasmid # 80806 (pME-mKate2 no stop) pcDNA3.1 EYFP H148Q/I152L Galietta et al., 2001 Addgene plasmid # 25872 (pcDNA3.1 EYFP H148Q/I152L) Software and Algorithms GraphPad Prism Version 8 GraphPad Software, San Diego, CA, USA www.graphpad.com Hybrid cell count BZ-H3C software Keyence, Osaka, Japan https://www.keyence.com/ Image Lab software Bio-Rad Laboratories, Inc., Hercules, CA, USA https://www.bio-rad.com/ Cell Chemical Biology 27, 1–11.e1–e6, December 17, 2020 e2 system, the normal-type splicing (skipping of the pseudo exon) leads to the expression of a GFP-fusion protein. ..
Expressing:Article Title: Mechanism-Based Personalized Medicine for Cystic Fibrosis by Suppressing Pseudo Exon Inclusion.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER pSS21_ CFTRWT-GFP (CFTR CDS+truncated IVS22 (WT) with N-terminal mKate2-GP2A and C-terminal HiBiTHA-AcGFP) This paper N/A pSS22_ CFTRC>T-GFP (CFTR CDS+truncated IVS22 (3849+10kb C>T) with N-terminal mKate2-GP2A and C-terminal HiBiT-HA-AcGFP) This paper N/A pSS23_ CFTRF508d-GFP (CFTR CDS (DF508 ) with N-terminal mKate2-GP2A and C-terminal AcGFP) This paper N/A CFTR WT_HiBiT Promega N/A (Gift from Promega) CFTR_delF508_HiBiT Promega N/A (Gift from Promega) pME-mKate2 no stop vector Fowler et al., 2016 Addgene plasmid # 80806 (pME-mKate2 no stop) pcDNA3.1 EYFP H148Q/I152L Galietta et al., 2001 Addgene plasmid # 25872 (pcDNA3.1 EYFP H148Q/I152L) Software and Algorithms GraphPad Prism Version 8 GraphPad Software, San Diego, CA, USA www.graphpad.com Hybrid cell count BZ-H3C software Keyence, Osaka, Japan https://www.keyence.com/ Image Lab software Bio-Rad Laboratories, Inc., Hercules, CA, USA https://www.bio-rad.com/ Cell Chemical Biology 27, 1–11.e1–e6, December 17, 2020 e2 system, the normal-type splicing (skipping of the pseudo exon) leads to the expression of a GFP-fusion protein. ..
Recombinant:Article Title: Different translation dynamics of β- and γ-actin regulates cell migration
Article Snippet: .. Recombinant DNA reagent pUbC-FLAG-24xSuntagV4oxEBFP-AID-baUTR124xMS2V5-Wpre (plasmid) Wu et al., 2016 Addgene plasmid # 84561 Plasmid containing Suntag, AID, b-actin 30UTR, MS2 repeats. ..
Article Title: Different translation dynamics of β- and γ-actin regulates cell migration
Article Snippet: .. Recombinant DNA reagent UbC NLS HA stdMCP stdHalo Voigt et al., 2017 Addgene plasmid # 104999 Plasmid containing MCP tandem dimer fused to HaloTag tandem dimer to visualize MS2 repeat containing RNA Recombinant DNA reagent pUbC-nls-hastdMCP-stdGFP Wu et al., 2016 Addgene plasmid # 98916 Plasmid containing MCP tandem dimer fused to GFP tandem dimer. ..
Article Title: TEMPO enables sequential genetic labeling and manipulation of vertebrate cell lineages.
Article Snippet: .. GCACATGTCG This manuscript PB-REV Recombinant DNA p5E-ubi Mosimann et al., 2011 Addgene Plasmid #27320; RRID: Addgene_27320 pDestTol2pA2 Kwan et al., 2007 #394 pME-MCS Kwan et al., 2007 #237 p3E-MCS Don et al., 2017 Addgene Plasmid #75174; RRID: Addgene_75174 ZebraF-Cassa-#3 Garcia-Marques et al., 2019 ZebraF-Cassa-#3 pME-H2B-mCerulean3 Don et al., 2017 Addgene plasmid #75156; RRID: Addgene_75156 pToneDest (pDesTol1) Shin et al., 2016 Addgene plasmid #67691; RRID: Addgene_67691 p5E-5xUAS vector Asakawa et al., 2008 p5E-5xUAS pME-zCas9 Ablain et al., 2015 Addgene plasmid # 63154; RRID: Addgene_63154 p5E-her4.1 Yeo et al., 2007 p5E-her4.1 pXL-CMV-piggyBac Transposagen Biopharmaceuticals Inc N/A pcDNA3.1/Puro-CAG-ASAP1 St-Pierre et al., 2014 Addgene plasmid # 52519; RRID: Addgene_52519 PB-CA-pDest Woltjen et al., 2009 Addgene plasmid # 20960; RRID: Addgene_20960 pX330-U6-Chimeric_BB-CBh-hSpCas9 Cong et al., 2013 Addgene plasmid # 42230; RRID: Addgene_42230 pCS2-Tol1.zf1 Horstick et al., 2015 Addgene plasmid # 61388; RRID: Addgene_61388 pCS2FA-transposase Clark et al., 2011 Tolkit plasmid #396 ubi:TEMPO-gRNA1_Tol1 This manuscript zTEMPO_1 ubi:TEMPO_Tol1 This manuscript zTEMPO_2 ubi:TEMPO-RFPon-gRNA2_Tol1 This manuscript zTEMPO_3 ubi:TEMPO-RFPon _Tol1 This manuscript zTEMPO_4 (Continued on next page) ll OPEN ACCESSNeuroResource Neuron 111, 345–361.e1–e10, February 1, 2023 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER ubi:TEMPO-RFPon-gRNA2switchgRNA1_Tol1 This manuscript zTEMPO_5 ubi:TEMPO-RFPon-gRNA2switch _Tol1 This manuscript zTEMPO_6 UAS:TEMPO-gRNA1_Tol1 This manuscript zTEMPO_7 TRE:TEMPO-gRNA1_Tol2 This manuscript zTEMPO_8 ubi:4-step-TEMPO-gRNA1_Tol2 This manuscript zTEMPO_9 ubi:4-step-TEMPO_Tol2 This manuscript zTEMPO_10 ubi:Cas9-H2B-Halotag-gRNA2switch_Tol1 This manuscript zTEMPO_11 ubi:Cas9-H2B-Halotag_gRNA3switch_Tol1 This manuscript zTEMPO_12 ubi:Cas9-H2B-Halotag_Tol1 This manuscript zTEMPO_13 ubi:Cas9gRNA3switch_gRNA2switch_Tol2 This manuscript zTEMPO_14 her4.1:Cas9-H2B-HalotaggRNA2switch_Tol1 This manuscript zTEMPO_15 TRE:Cas9-H2B-HalotaggRNA2switch_Tol1 This manuscript zTEMPO_16 ubi:Gal4-gRNA2switch_Tol2 This manuscript zTEMPO_17 her4.1:tTA_Tol2 This manuscript zTEMPO_18 pCS2-Gal4ff.zf1 Horstick et al., 2015 Addgene plasmid # 61392; RRID: Addgene_61392 pTet-Off Advanced Vector Takara Cat#631070 CAG-PB This manuscript #406 CAG:TEMPO-gRNA1_PB This manuscript mTEMPO_1 CAG:4-step-TEMPO-gRNA1_PB This manuscript mTEMPO_2 CAG:TEMPO-T1CD1-gRNA1_PB This manuscript mTEMPO_3 CAG:TEMPO-T2CD1-gRNA1_PB This manuscript mTEMPO_4 CAG:TEMPO-T3CD1-gRNA1_PB This manuscript mTEMPO_5 CAG:TEMPO-AllFramesCD1-gRNA1_PB This manuscript mTEMPO_6 CAG:TEMPO-T1CB1-gRNA1_PB This manuscript mTEMPO_7 CAG:TEMPO-T2CB1-gRNA1_PB This manuscript mTEMPO_8 CAG:Cas9-H2BHalotag_gRNA2switch_PB This manuscript mTEMPO_9 gRNAswitch3_CAG:Cas9_ gRNA2switch_PB This manuscript mTEMPO_10 Episomal CAG-Halotag This manuscript mTEMPO_11 Software and algorithms Fiji (ImageJ version 2.0.0-rc-68/1.52e) NIH RRID: SCR_002285 Benchling Benchling platform RRID: SCR_013955 Adobe Illustrator CC 2018 Adobe RRID: SCR_010279 Other cell culture insert Millipore PICM0RG50 ll OPEN ACCESS NeuroResource
Article Title: A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-H3K27ac Abcam Cat# ab4729, RRID: AB_2118291 Mouse monoclonal anti-CD24 APC-eFluor 780 Thermo Fisher Scientific Cat# 47-0242-82, RRID: AB_10853172 Chicken polyclonal anti-GFP Thermo Fisher Scientific Cat# A10262, RRID: AB_2534023 Rabbit polyclonal anti-RFP Abcam Cat# ab62341, RRID: AB_945213 Rabbit polyclonal anti-Tet1 GeneTex Cat# GTX125888, RRID:AB_11164485 Mouse polyclonal anti-Dnmt3a Novus Biological Cat# NB120-13888, RRID: AB_789607 Mouse anti-Isl1/2 Jessell Lab/HHMI CU RRID: AB_2314683 Chemicals, peptides, and recombinant proteins Lipofectamine 2000 Invitrogen Cat# 11668019 T7 endonuclease NEB Cat# M0302L Protein G Dynabeads Invitrogen Cat# 10004D Ampure XP beads Beckman Coulter Cat# A63880 Di(N-succinimidyl) glutarate (DSG) Sigma Cat# 80424 Retinoic acid Sigma Cat# R2625 Deposited data Raw and analyzed allele-specific 4C-seq data This paper GSE148315 Mouse reference genome GRCm38 (mm10) Genome Reference Consortium https://www.ncbi.nlm.nih.gov/assembly/ GCF_000001635.20/ Experimental models: Cell lines Mouse B6J: iPSC Dlk1matVenus/patTomato, clone #6aa Swanzey and Stadtfeld, 2016 N/A Mouse matJF1/patB6N/J: iPSC Dlk1matTomato/patVenus, clone #104 This paper N/A Dnmt3ab KO ESCs, clone DKO#9 Lei et al., 1996 N/A Tet1/2/3 KO ESCs, clone TKO#9 Dawlaty et al., 2014 N/A Tet1/2/3 WT ESCs, clone WT#8 Dawlaty et al., 2014 N/A Oligonucleotides See Table S1 gRNAs and primer sequences N/A N/A Recombinant DNA pdCas9-Dnmt3a-puro Vojta et al., 2016 Addgene Plasmid #71667 pPGKENTRY-dCas9-Tet1CD Verma et al., 2018 N/A pMIGR1-IRES-BSD This paper N/A pBS-Dlk1-tomato Swanzey and Stadtfeld, 2016 N/A pHR-SFFV-dCAS9-BFP-KRAB Gilbert et al., 2013 Addgene Plasmid #46911 pLKO5.sgRNA.EFS.PAC Heckl et al., 2014 Addgene Plasmid #57825 pSpCas9(BB)-2A-GFP (pX458) Ran et al., 2013 Addgene Plasmid #48138 pHR-EF1a-dCAS9-Dnmt3a-BSD This paper N/A pHR-EF1a-dCAS9-Tet1-BSD This paper N/A pLKO5.sgRNA.EFS.PAC - F+E - Neo This paper N/A pHR-EF1a-dCAS9-BFP-KRAB This paper N/A pX330-PGK-NeoR Cong et al., 2013 Addgene Plasmid #42230 (Continued on next page) e1 Developmental Cell 56, 3052–3065.e1–e5, November 22, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms FlowJo (v10.7.0) BD Biosciences http://v9docs.flowjo.com/html/index.html RRID: SCR_008520 IGV browser Robinson et al., 2011 https://software.broadinstitute.org/ software/igv/ RRID:SCR_011793 Samtools (v1.8) Li et al., 2009 http://samtools.sourceforge.net/ RRID:SCR_002105 ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ RRID:SCR_003070 GraphPad Prism GraphPad http://www.graphpad.com/ RRID:SCR_002798
other:Article Title: HOXA9 promotes MYC-mediated leukemogenesis by maintaining gene expression for multiple anti-apoptotic pathways
Article Snippet: (species) or resource Designation Source or reference Identifiers Additional information Antibody MCL1 (Rabbit monoclonal, D35A5) Cell Signaling Technology Cat# 5453 RRID:AB_10694494 WB (1:2000) Antibody APC Annexin V BD Biosciences Cat# 550475 RRID:AB_2868885 FACS (1:100) Antibody Propidium iodide Thermo Fisher Scientific P3566 FACS (1:2000) Antibody Gr-1 (Rat monoclonal, RB6-8C5) BD Biosciences Cat# 553127 RRID:AB_394643 FACS (1:100) Antibody B220 (Rat monoclonal, RA3-6B2) BD Biosciences Cat#: 553088 RRID:AB_394618 FACS (1:100) Antibody TER119 (Rat monoclonal, TER-119) BD Biosciences Cat#: 557915 RRID:AB_396936 FACS (1:100) Antibody CD3e (Hamster monoclonal, 145– 2 C11) BD Biosciences Cat#: 553062 RRID:AB_394595 FACS (1:100) Antibody Mac/CD11b (Rat monoclonal, M1/70) BD Biosciences Cat#: 553310 RRID:AB_394774 FACS (1:100) Antibody c-Kit (Rat monoclonal, 2B8) BD Biosciences Cat#: 553355 RRID:AB_394806 FACS (1:100) Antibody Sca1 (Rat monoclonal, D7) BD Biosciences Cat#: 553108 RRID:AB_394629 FACS (1:100) Antibody CD34 (Rat monoclonal, RAM34) BD Biosciences Cat#: 751621 RRID:AB_2875614 FACS (1:100) Antibody CD16/32 (Rat monoclonal, 93) BD Biosciences Cat#: 751690 RRID:AB_2875675 FACS (1:100) Recombinant DNA reagent pMSCV-neo Clontech Cat#: 634401 Gene expression vector Recombinant DNA reagent pMSCV-puro Clontech Cat#: 634401 Gene expression vector Recombinant DNA reagent pMSCV-hygro Clontech Cat#: 634401 Gene expression vector Recombinant DNA reagent pLKO5.EFS.GFP Addgene (gift from Benjamin Ebert) Heckl et al., 2014 Addgene Plasmid #57822 RRID:Addgene_57822 sgRNA backbone Recombinant DNA reagent pKLV2-Cas9.bsd Addgene (gift from Kosuke Yusa) Tzelepis et al., 2016 Addgene Plasmid #68343 RRID:Addgene_68343 Cas9 expression vector Recombinant DNA reagent pMDLg/pRRE Addgene (gift from Didier Trono) Dull et al., 1998 Addgene Plasmid #12251 RRID:Addgene_12251 Lentivirus packaging vector
Article Title: Activation of CpG-Rich Promoters Mediated by MLL Drives MOZ-Rearranged Leukemia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Fluoppi Ver.2 MBL Cat#AM-8011M RNeasy Mini Kit QIAGEN Cat#74106 SuperScript III First-Strand cDNA Synthesis System Thermo Fisher Scientific Cat#18080051 SureSelect Strand Specific RNA Library Prep Kit Agilent Technologies Cat#G9691A TruSeq ChIP Sample Prep Kit SetB Illumina Cat#IP-202-1024 Unmethyl Collector Kit Active Motif Discontinued c-Kit magnetic beads Miltenyi Biotec Cat#130-091-224 Deposited Data ChIP-seq data of HB1119 cells, see Table S3 The DDBJ Sequence Read Archive DRA002840, DRA004871, DRA008735 ChIP-seq data of HEK293T cells, see Table S3 The DDBJ Sequence Read Archive DRA004872, DRA008732, DRA008733, DRA010562, DRA010563, ChIP-seq data of REH cells, see Table S3 The DDBJ Sequence Read Archive DRA010564 CIRA-seq data of HB1119 cells, see Table S4 The DDBJ Sequence Read Archive DRA010565 CIRA-seq data of HB1119 cells, see Table S4 The DDBJ Sequence Read Archive DRA008734 RNA-seq data, see Table S5 The DDBJ Sequence Read Archive DRA004874 Experimental Models: Cell Lines Human: HB1119 Laboratory of Michael Clearly (Tkachuk et al., 1992) N/A Human: HEK293T Laboratory of Michael Cleary (Yokoyama et al., 2004) Authenticated by JRCB cell bank in 2019 Human: REH Laboratory of Michael Cleary (Yokoyama et al., 2004) N/A Human: HEK293T dMLLc3 This paper N/A Human: HEK293T dMLLc7 This paper N/A Human: HEK293TL Okuda et al., 2015 N/A Human: PLAT-E Laboratory of Toshio Kitamura (Morita et al., 2000) N/A Experimental Models: Organisms/Strains Mouse: C57BL/6J CLEA Japan, Inc. N/A Oligonucleotides Oligos for sgRNA, see Table S1 This paper N/A Primers for qPCR, see Table S2 This paper N/A Recombinant DNA pCMV5 Laboratory of Michael Cleary N/A pKLV2-EF1a-Cas9Bsd-W Tzelepis et al., 2016 Addgene Plasmid #68343 pLKO-puro-FR-LUC Okuda et al., 2015 N/A pLKO5.sgRNA.EFS.GFP Heckl et al., 2014 Addgene Plasmid #57822 pMD2.G Dull et al., 1998 Addgene Plasmid #12259 pMDLg/pRRE Dull et al., 1998 Addgene Plasmid #12251 pMSCV Clontech 634401 pRSV-rev Dull et al., 1998 Addgene Plasmid #12253 pX335-U6-Cgumeric_BB-CBh-hSpCas9n (D10A) Cong et al., 2013 Addgene Plasmid #42335 pcDNA4 HisMax Invitrogen V86420 Software and Algorithms BWA Li and Durbin, 2009 http://bio-bwa.sourceforge.net Cutadapt Martin, 2011 https://cutadapt.readthedocs.io/ en/stable/index.html FlowJo BD Biosciences N/A (Continued on next page) e2 Cell Reports 32, 108200, September 29, 2020
Digital PCR:Article Title: iPSC modeling of stage-specific leukemogenesis reveals BAALC as a key oncogene in severe congenital neutropenia.
Article Snippet: 2013 Addgene Plasmid # 48138 pCMV-BE3 Komor A et al., Nature. .. 2016 Addgene Plasmid #73021 BAALC_p.19.NLS.BE3.2xNLS.GFP.PX458 This paper N/A Software and algorithms GraphPad Prism 8 GraphPad Software Inc. https://www.graphpad.com/ FlowJo V10 BD https://www.flowjo.com/ QuantStudio 3D Digital PCR Analysis Suite Software Thermo Fisher https://www.thermofisher.com/us/en/home/ life-science/pcr/digital-pcr/quantstudio-3ddigital-pcr-system/quantstudio-3d-software.html Connectivity map (CMAP) CLUE platform https://clue.io/cmap Feature Extraction Software Agilent Technologies https://www.agilent.com/en/product/mirna- microarray-platform/mirna-microarraysoftware/feature-extraction-software-228496 Agilent Genomic-Workbench Agilent Technologies https://www.agilent.com/en/product/cgh- cgh-snp-microarray-platform/cgh-cgh-snpmicroarray-software/agilent-genomicworkbench-228497 CRISPOR Concordet J et al., Nucleic Acid Research. ..
Extraction:Article Title: iPSC modeling of stage-specific leukemogenesis reveals BAALC as a key oncogene in severe congenital neutropenia.
Article Snippet: 2013 Addgene Plasmid # 48138 pCMV-BE3 Komor A et al., Nature. .. 2016 Addgene Plasmid #73021 BAALC_p.19.NLS.BE3.2xNLS.GFP.PX458 This paper N/A Software and algorithms GraphPad Prism 8 GraphPad Software Inc. https://www.graphpad.com/ FlowJo V10 BD https://www.flowjo.com/ QuantStudio 3D Digital PCR Analysis Suite Software Thermo Fisher https://www.thermofisher.com/us/en/home/ life-science/pcr/digital-pcr/quantstudio-3ddigital-pcr-system/quantstudio-3d-software.html Connectivity map (CMAP) CLUE platform https://clue.io/cmap Feature Extraction Software Agilent Technologies https://www.agilent.com/en/product/mirna- microarray-platform/mirna-microarraysoftware/feature-extraction-software-228496 Agilent Genomic-Workbench Agilent Technologies https://www.agilent.com/en/product/cgh- cgh-snp-microarray-platform/cgh-cgh-snpmicroarray-software/agilent-genomicworkbench-228497 CRISPOR Concordet J et al., Nucleic Acid Research. ..
Microarray:Article Title: iPSC modeling of stage-specific leukemogenesis reveals BAALC as a key oncogene in severe congenital neutropenia.
Article Snippet: 2013 Addgene Plasmid # 48138 pCMV-BE3 Komor A et al., Nature. .. 2016 Addgene Plasmid #73021 BAALC_p.19.NLS.BE3.2xNLS.GFP.PX458 This paper N/A Software and algorithms GraphPad Prism 8 GraphPad Software Inc. https://www.graphpad.com/ FlowJo V10 BD https://www.flowjo.com/ QuantStudio 3D Digital PCR Analysis Suite Software Thermo Fisher https://www.thermofisher.com/us/en/home/ life-science/pcr/digital-pcr/quantstudio-3ddigital-pcr-system/quantstudio-3d-software.html Connectivity map (CMAP) CLUE platform https://clue.io/cmap Feature Extraction Software Agilent Technologies https://www.agilent.com/en/product/mirna- microarray-platform/mirna-microarraysoftware/feature-extraction-software-228496 Agilent Genomic-Workbench Agilent Technologies https://www.agilent.com/en/product/cgh- cgh-snp-microarray-platform/cgh-cgh-snpmicroarray-software/agilent-genomicworkbench-228497 CRISPOR Concordet J et al., Nucleic Acid Research. ..
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