Thread View: bionet.organisms.zebrafish
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Started by Keith Joung
Wed, 21 Nov 2012 00:57
Announcement of FOURTH Solicitation for NIH-funded Resource to Target Zebrafish Genes with Engineered Nucleases
Author: Keith Joung
Date: Wed, 21 Nov 2012 00:57
Date: Wed, 21 Nov 2012 00:57
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Dear Colleagues, We are writing again to solicit recommendations for appropriate genes to target in our FOURTH solicitation of zebrafish genes to target with engineered nucleases and we plan to construct 96 TALEN pairs for this new round. As many of you know, we have previously made three solicitations to the community regarding the construction of engineered zinc finger pairs for endogenous zebrafish gene targets. As a result of these efforts, out of 192 zebrafish genes we have targeted to date, we have successfully constructed zinc finger pairs for 49 zebrafish genes and TALEN pairs for 84 zebrafish genes with TALEN pairs for 20 more genes to be completed in the coming weeks. Plasmids encoding these completed zinc fingers and TALENs have been deposited with the non- profit plasmid distribution service Addgene (http://www.addgene.org/ zfc/arrays/ for the zinc fingers and http://www.addgene.org/talengineering/TALENzebrafish/ for the TALENs). Note that the newest TALEN pairs will be available in the coming weeks after Addgene has sequence-verified the plasmids. Each laboratory may submit up to TWO gene targets by completing the Excel request form (available for download here: http://www.talengineering.org/download.htm) -- one gene recommendation should be placed on each of the "Sheets" in the file. Place your first choice gene on the first sheet and your second choice gene on the second sheet. Please note that ALL required fields must be filled out � we will not accept or consider any incomplete forms. For a gene to be considered appropriate for this effort, we ask each recommender to verify on the form that mutations in the gene of interest do not already exist and that efforts to generate mutations in the recommended gene are not underway elsewhere. VERY IMPORTANT NOTE: Each gene submitted MUST include its Ensembl Gene ID (ENSDARG) the Ensembl Transcript ID (ENSDART), and the gene name (e.g.-- Example: ENSDARG00000024771, ENSDART00000033574, slc24a5). In the event that Ensembl has incorrectly annotated the gene of interest, the full genomic sequence of your gene should be included with exons denoted by upper case and introns in lower case. Genes not correctly submitted in one of these formats will NOT be considered for targeting. Recommendations will be considered in the order in which they are received. We will choose one gene for targeting from each lab until we reach 96 gene targets. If we receive fewer than 96 targetable "first choice" gene requests, we will then consider �second choice� requests in the order in which we received the e-mails until we reach 96 gene targets. Please note that we plan to make another FIFTH solicitation in the spring of 2013. Please e-mail your completed form to zebrafishzfs@zincfingers.org at or after (and not before) 12:00 Noon (Eastern US time) November 30th, 2012. Requests received before this date/time will not be considered. Gene recommendations will only be accepted via e-mail. Note that recommendations from scientists at commercial entities will not be accepted. With best regards, Keith Joung Randall Peterson Joanna Yeh Jeffry Sander Deepak Reyon Jon Foley Massachusetts General Hospital
Re: Announcement of FOURTH Solicitation for NIH-funded Resource to Target Zebrafish Genes with Engineered Nucleases
Author: Keith Joung
Date: Sun, 06 Jan 2013 23:50
Date: Sun, 06 Jan 2013 23:50
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Dear all, Listed below are the 96 zebrafish genes and target sites for which we will make FLASH-assembled TALENs for the community as part of our NIH- sponsored initiative. We hope to deposit the plasmids encoding these TALENs with Addgene by February 2013. We will write with updates as we make those deposits. Best, Keith Joung Randall Peterson Joanna Yeh Jeffry Sander Deepak Reyon Jon Foley Massachusetts General Hospital TALEN # Targetsitename TALEN (5' to 3') 1 ZebrafishCommunity-aak1-left TCTTTGACTCCCGGAGAG 1 ZebrafishCommunity-aak1-right TCCCCCTCCAGAACCTGG 2 ZebrafishCommunity-amh-left TCCAGGCAAGATTTGGGC 2 ZebrafishCommunity-amh-right TACGACCCAATCGCCACG 3 ZebrafishCommunity-arf6-left TGGGGAAGATGCTTTCCA 3 ZebrafishCommunity-arf6-right TCAATATTCTCATCTCC 4 ZebrafishCommunity-arnt1-left TCCCGTCTCTGGCCATGA 4 ZebrafishCommunity-arnt1-right TGCACACCGTTGGAATGA 5 ZebrafishCommunity-atg12-left TTAATCAGTCGTTTGCGC 5 ZebrafishCommunity-atg12-right TCAAAAAGCACACCAACT 6 ZebrafishCommunity-atg5-left TAAAGTCAAGAAACATTT 6 ZebrafishCommunity-atg5-right TTCCTCCACATCCTCTGC 7 ZebrafishCommunity-avpl-left TGCTGTGTGTGCTCGCGC 7 ZebrafishCommunity-avpl-right TTCTGGATGTAGCAGGCA 8 ZebrafishCommunity-Ccl2-left TTTTCGTTTTCCACTATA 8 ZebrafishCommunity-Ccl2-right TATGATAACTCTGAACCT 9 ZebrafishCommunity-cebpb-left TGGAAGTGGCCGGTTTTT 9 ZebrafishCommunity-cebpb-right TTAGTGCTGTGGAAAGCG 10 ZebrafishCommunity-CIT1-left TGAAGTTTAAATATGGAG 10 ZebrafishCommunity-CIT1-right TCGACTGCGGACAGATCT 11 ZebrafishCommunity-cited2-left TGGTAGACCGCATGATGG 11 ZebrafishCommunity-cited2-right TTCACAGCATCTGGGAAA 12 ZebrafishCommunity-ComplementFactorH-left TGATTACATGTGAACCTC 12 ZebrafishCommunity-ComplementFactorH-right TCCAAAAGGAGGTGGACA 13 ZebrafishCommunity-crispld2-left TATCAGGAGGAGCTAGAA 13 ZebrafishCommunity-crispld2-right TTCGGACAGGAGCGTCGG 14 ZebrafishCommunity-dachc-left TCCAGACCTGGCAGACCT 14 ZebrafishCommunity-dachc-right TGTCGGGTGATGTCACAT 15 ZebrafishCommunity-dbx1b-left TCCCGTGCAAGGAATGAA 15 ZebrafishCommunity-dbx1b-right TCCGTCAAAACAAGGGAA 16 ZebrafishCommunity-DGKE-left TATGGTGTCAAACCACAG 16 ZebrafishCommunity-DGKE-right TCATCGGTCAGACTGGAA 17 ZebrafishCommunity-Dlk1-left TGGTGGCGCAGCAGAGGG 17 ZebrafishCommunity-Dlk1-right TGATGTTCACGGTGGCC 18 ZebrafishCommunity-Dlk2-left TTGGCCACGGAAAATGTG 18 ZebrafishCommunity-Dlk2-right TCCCGGATCACACCTG 19 ZebrafishCommunity-drd4b-left TTCACTTACAATGTTCCC 19 ZebrafishCommunity-drd4b-right TAACAATGATAAGCAATA 20 ZebrafishCommunity-EMP2-left TCAGGCAGTGCAGGCCAC 20 ZebrafishCommunity-EMP2-right TCCCACACAGCACAAGAT 21 ZebrafishCommunity-eps15-left TTGCCCATTGCCTATCGC 21 ZebrafishCommunity-eps15-right TAGTGTTTCTGTTCCCAC 22 ZebrafishCommunity-esr1-left TCAGTGGGATACTACCCG 22 ZebrafishCommunity-esr1-right TCTGTAGATGTTCCTCGT 23 ZebrafishCommunity-fam123b-left TGGAGATCGCCACAAGAT 23 ZebrafishCommunity-fam123b-right TCTGACGATGGACCCCTC 24 ZebrafishCommunity-fgfbp1a-left TGTCTCTCCGCGGAATTT 24 ZebrafishCommunity-fgfbp1a-right TGTGAGACGCACGCGAGA 25 ZebrafishCommunity-foxl2-left TAACGGCATGATACTCAT 25 ZebrafishCommunity-foxl2-right TCGGTCTTTCTCCGCTGA 26 ZebrafishCommunity-FoxP1b-left TCGGGGACAGAGGCGGCA 26 ZebrafishCommunity-FoxP1b-right TGGGCGGAGCGCCGTTCT 27 ZebrafishCommunity-foxp3a-left TGCTTCTTAATGCTACTG 27 ZebrafishCommunity-foxp3a-right TGACTACTCCTGTTATCA 28 ZebrafishCommunity-Frizzled5-left TCGGATTTTGGCTGCATG 28 ZebrafishCommunity-Frizzled5-right TCTCCGAGCCCAGACAGT 29 ZebrafishCommunity-Fryl-left TTCCAGGCGGTGCGTAAG 29 ZebrafishCommunity-Fryl-right TCAGCCTCAGTTCCTTCA 30 ZebrafishCommunity-fscn2a-left TAAATCACGAAAATCGAT 30 ZebrafishCommunity-fscn2a-right TTGATCTTGAAACCAAAT 31 ZebrafishCommunity-GnIH-left TGTAAGATGTCCTACTTC 31 ZebrafishCommunity-GnIH-right TGCTCAGGATGCCGAGGG 32 ZebrafishCommunity-GnRH3-left TTGGAGGTCAGTCTTTGC 32 ZebrafishCommunity-GnRH3-right TTCCACCGGGAAGCCAAC 33 ZebrafishCommunity-gper-left TGGAGGAGCAGACTACCA 33 ZebrafishCommunity-gper-right TGCTCGGTGCCATTCACA 34 ZebrafishCommunity-hemogen-site1-left TGGAAGACCCGTTGGAGA 34 ZebrafishCommunity-hemogen-site1-right TCTGAATCTTTTATTTCA 35 ZebrafishCommunity-hemogen-site2-left TGATTTGTTTGTTTGCT 35 ZebrafishCommunity-hemogen-site2-right TCTCTGTCTCTGAGTCG 36 ZebrafishCommunity-hif1al-site1-left TGTTTCAGCAGAGCCCCG 36 ZebrafishCommunity-hif1al-site1-right TCCACTCCTTCCATCTCC 37 ZebrafishCommunity-hif1al-site2-left TGCCCTCAGGACTTCTGC 37 ZebrafishCommunity-hif1al-site2-right TATTGGAGACAGAAGCT 38 ZebrafishCommunity-hirip3-left TGGCCAAAGAAAAGGACG 38 ZebrafishCommunity-hirip3-right TTCTGCAGTTGAGCCACA 39 ZebrafishCommunity-hist2h3ca1-left TCTGTTTGAGGACACCAA 39 ZebrafishCommunity-hist2h3ca1-right TGATGGTGACCCTCTTGG 40 ZebrafishCommunity-hnrnpr-left TGGATGCGGGTCTGCCCC 40 ZebrafishCommunity-hnrnpr-right TGGAAGATGTTATCCAGG 41 ZebrafishCommunity-hnrnpu-left TTAAGGTGAACGAGCTGA 41 ZebrafishCommunity-hnrnpu-right TTGTCAGAGAGCTGCCGC 42 ZebrafishCommunity-hs3st1l1-left TCTTCTGAGTTATGTGTT 42 ZebrafishCommunity-hs3st1l1-right TGGAGGAGCGGCGTATGC 43 ZebrafishCommunity-hs3st1-left TCAATCCTCTGTCCTGGT 43 ZebrafishCommunity-hs3st1-right TAGCGCAGCATCAGGCGG 44 ZebrafishCommunity-Id4-left TTTATTACAATGAAGGCC 44 ZebrafishCommunity-Id4-right TAGAAGGAAGCTTATGAG 45 ZebrafishCommunity-IPIP27A-left TGAACGAGAGGAGTGTGG 45 ZebrafishCommunity-IPIP27A-right TTGTCTGGAGGAGAGTTG 46 ZebrafishCommunity-jarid2a-left TGGGATCCCGTGGTCAGA 46 ZebrafishCommunity-jarid2a-right TGAGAGGTAGAGCACCCG 47 ZebrafishCommunity-lhx1a-left TTTATCGGACAAAGAAAC 47 ZebrafishCommunity-lhx1a-right TCCAAGGTTCTGGTCATC 48 ZebrafishCommunity-lrrtm1-left TCTAATTGGTCTGTACCT 48 ZebrafishCommunity-lrrtm1-right TATCAGCCCAGGGGGCTT 49 ZebrafishCommunity-mak-left TCAAGCAGCTGGGTGATG 49 ZebrafishCommunity-mak-right TTGCTCTTCCCCATTAGA 50 ZebrafishCommunity-mapk14a-left TCTTCTTGTGCTCTTATT 50 ZebrafishCommunity-mapk14a-right TCAGCGCCCATAAGGTGA 51 ZebrafishCommunity-max-left TGAGCGACAACGATGA 51 ZebrafishCommunity-max-right TAACTATACTCACATC 52 ZebrafishCommunity-mchr1a-left TGGCCATCTGTTTGGCCT 52 ZebrafishCommunity-mchr1a-right TGAAGGATGTAATATGGA 53 ZebrafishCommunity-mef2aa-left TGGGACGGAAGAAGATAC 53 ZebrafishCommunity-mef2aa-right TGCCGGTTCCTCTCATCC 54 ZebrafishCommunity-meis2a-left TGAGCTGGCTCACTACGG 54 ZebrafishCommunity-meis2a-right TGGATCCCCGTACATCCC 55 ZebrafishCommunity-meis4.1a-left TACGAGGATCTGGTCCAC 55 ZebrafishCommunity-meis4.1a-right TCGGAGACGGGATCCCGA 56 ZebrafishCommunity-mrc1a-left TGTTGTACAAGGGATCAG 56 ZebrafishCommunity-mrc1a-right TTGGTCCCATACACCTGC 57 ZebrafishCommunity-NPVF-left TTAGCCCTCGGCATCCTG 57 ZebrafishCommunity-NPVF-right TGAGAGCCGTAACTTCAC 58 ZebrafishCommunity-nr5a2-left TGGACTACTCCTACGACG 58 ZebrafishCommunity-nr5a2-right TCTCCGCACACTGGACAC 59 ZebrafishCommunity-nup155-left TCGCTGTCTGGCGTGTCC 59 ZebrafishCommunity-nup155-right TCAGCGCGGGACCCTGCA 60 ZebrafishCommunity-NUPL2-left TGGATAAACCCATCTCAG 60 ZebrafishCommunity-NUPL2-right TGCCCCCTGCTGACGAGG 61 ZebrafishCommunity-ovol1-left TGTTCCAGTTCCAGCGCA 61 ZebrafishCommunity-ovol1-right TGCTCGCTGTGACATTTC 62 ZebrafishCommunity-oxtr-left TTCAAGGATCAAGACTTT 62 ZebrafishCommunity-oxtrl-left TGATCCTCTGGCCCATTA 63 ZebrafishCommunity-oxtrl-right TCGTTTCCCCTACTTGAG 63 ZebrafishCommunity-oxtr-right TGGTGGCGTTTCTGGATG 64 ZebrafishCommunity-park2-left TGATCGTTTTCGTGCGGT 64 ZebrafishCommunity-park2-right TCCAACTCCACCGGGAAC 65 ZebrafishCommunity-pcolce2b-left TCCTCACATTTCGTTTCC 65 ZebrafishCommunity-pcolce2b-right TCGTACCGACACAGGTTG 66 ZebrafishCommunity-pink1-left TTTCCTCTCATAGTCAAT 66 ZebrafishCommunity-pink1-right TTTACTGACATTTTGAGC 67 ZebrafishCommunity-Popdc2-left TGAATTGGAGACAGCAGA 67 ZebrafishCommunity-Popdc2-right TCAATGAAGAGTCGCCGC 68 ZebrafishCommunity-Popdc3-left TCTCACTGTTAAGATTAT 68 ZebrafishCommunity-Popdc3-right TATTCTCAGGTAAAAGAT 69 ZebrafishCommunity-prothymosinalphaa-left TTATCATTCGCATCTCGT 69 ZebrafishCommunity-prothymosinalphaa-right TGGGGTCTCGGAATAAAA 70 ZebrafishCommunity-prrx1b-left TAATACACTTGCCAATTT 70 ZebrafishCommunity-prrx1b-right TGCATAGCTAGAAGTCAT 71 ZebrafishCommunity-PurinergicreceptorY2-left TTCAACGCATCAGTGAAT 71 ZebrafishCommunity-PurinergicreceptorY2-right TGCTGCAGCTGTGTGCAG 72 ZebrafishCommunity-rassf7b-left TGAAGGTGTGGGTGGATG 72 ZebrafishCommunity-rassf7b-right TCTTCTGAGAGGCCACAG 73 ZebrafishCommunity-scrt2-left TTTTCTGGTGCGTCTGTG 73 ZebrafishCommunity-scrt2-right TCACCAGAAACGAGCGAG 74 ZebrafishCommunity-sema6dl-left TGCTGATACTCCTGCTGG 74 ZebrafishCommunity-sema6dl-right TCAGGAAAGCTCACAGCA 75 ZebrafishCommunity-Semaphorin6bb-left TTGAAAAGTGCTGAGAAA 75 ZebrafishCommunity-Semaphorin6bb-right TTTGTCTCCTAAATCAAA 76 ZebrafishCommunity-si:ch211-120j21.1-left TGAACTGTCAGTCGGGAC 76 ZebrafishCommunity-si:ch211-120j21.1-right TGAAAGAAAGCGCATAAA 77 ZebrafishCommunity-slc50a1-left TTTCTGCAGCTGCTATCA 77 ZebrafishCommunity-slc50a1-right TGAACATCCCGACGGTGA 78 ZebrafishCommunity-snrnp35-left TCCGGTGGCGAAGGTGTA 78 ZebrafishCommunity-snrnp35-right TGTGCCGTCAATGCTGCC 79 ZebrafishCommunity-snrnp48-left TGTGTGAAACATCGTTTG 79 ZebrafishCommunity-snrnp48-right TGAAGACACTGCATGCGC 80 ZebrafishCommunity-sox1a-left TATAGCATGATGATGGAA 80 ZebrafishCommunity-sox1a-right TGTTGGTTTGGGGTCCCG 81 ZebrafishCommunity-Sox2-left TGGTGGGGTAGACTTTCG 81 ZebrafishCommunity-Sox2-right TTTCCATCATGTTATACA 82 ZebrafishCommunity-Tac3b-left TCCACGTGCTGCTGCTGC 82 ZebrafishCommunity-Tac3b-right TCGAGGGCGCTCCGCGAG 83 ZebrafishCommunity-taok2b-left TGCGGGCTGGGAGTCTCA 83 ZebrafishCommunity-taok2b-right TCCTTGTAAAAAAGTTCC 84 ZebrafishCommunity-tcof-left TAAAGACTCCTCCACCAG 84 ZebrafishCommunity-tcof-right TCACTACTGGACACTGCA 85 ZebrafishCommunity-tet2(ENSDART00000113020)-left TCAAGACCAGATACTATC 85 ZebrafishCommunity-tet2(ENSDART00000113020)-right TTCAGTAGGTGGTAGCTG 86 ZebrafishCommunity-tet3(ENSDART00000137355)-left TTGCTCCTTGGTTGCATC 86 ZebrafishCommunity-tet3(ENSDART00000137355)-right TAATGAAGAAAATGTTTG 87 ZebrafishCommunity-tfe3a-left TAAAATAGCCAGTCAGA 87 ZebrafishCommunity-tfe3a-right TGAGGGCTGTGGTGGG 88 ZebrafishCommunity-tfe3b-left TCGCTCAGCTCCGCCCT 88 ZebrafishCommunity-tfe3b-right TGGCAGCGAGACGGAGAT 89 ZebrafishCommunity-tnfb-left TGTCGGGGGAGTTTATCA 89 ZebrafishCommunity-tnfb-right TGAAGAATTAACCGGTAC 90 ZebrafishCommunity-TRABD2A-left TCAGCTGGAGCGCTTTTC 90 ZebrafishCommunity-TRABD2A-right TTTGCTCTCACCATGAGT 91 ZebrafishCommunity-TTC19-left TGCCAGGAGGAGCAGGGA 91 ZebrafishCommunity-TTC19-right TCACTCATCAGGACCAGC 92 ZebrafishCommunity-Vangl1-left TTCTCTGCCCAGGATAG 92 ZebrafishCommunity-Vangl1-right TGTCAGTAAACCCAGC 93 ZebrafishCommunity-vasa-left TGACTGGGAGGAAGATCA 93 ZebrafishCommunity-vasa-right TCCAAATCCTGAGCTGCA 94 ZebrafishCommunity-Vrk2-left TGTACTTGGCTGACTATG 94 ZebrafishCommunity-Vrk2-right TGCTCGCCATTAGGACAG 95 ZebrafishCommunity-ywhai-left TACAAGAATGTGGTGGGA 95 ZebrafishCommunity-ywhai-right TGCTGGACACTACCCTCC 96 ZebrafishCommunity-zmynd11-left TATGTTTGGTCGGCCATC 96 ZebrafishCommunity-zmynd11-right TGTTGGCGATTTGTTTCT
Re: Announcement of FOURTH Solicitation for NIH-funded Resource to Target Zebrafish Genes with Engineered Nucleases
Author: Keith Joung
Date: Fri, 01 Mar 2013 02:41
Date: Fri, 01 Mar 2013 02:41
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Dear Colleagues, I'm pleased to provide an update on our construction of engineered TALENs for our FOURTH NIH-sponsored solicitation of zebrafish gene targets. We now have sequence-verified plasmids encoding TALEN pairs for 94 of the 96 genes we targeted. The names of these 94 genes are listed below. We are still awaiting plasmids for the NPVF and oxtr genes and hope to provide an update on these shortly. All of these plasmids will be deposited with Addgene in the coming days and, after they pass Addgene's quality control checks, will be made available here: http://www.addgene.org/talengineering/TALENzebrafish/. The deposit of these new TALEN pairs will bring the total number of zebrafish genes targeted with engineered nucleases by this effort to nearly 250. An announcement regarding the next 96 genes to be targeted in our FIFTH solicitation will be made in the coming days. With best regards, Keith Joung Randy Peterson Joanna Yeh Jon Foley Deepak Reyon Jeff Sander Massachusetts General Hospital 94 new genes for which TALENs have been completed: aak1(1of2) amh arf6 arnt1 atg12 atg5 avpl Ccl2 cebpb CIT1 cited2 ComplementFactorH crispld2 dachc dbx1b DGKE Dlk1 Dlk2 drd4b EMP2 eps15 esr1 fam123b fgfbp1a foxl2 FoxP1b foxp3a Frizzled5 Fryl fscn2a GnIH GnRH3 gper hemogen-site1 hemogen-site2 hif1al-site1 hif1al-site2 hirip3 hist2h3ca1 hnrnpr hnrnpu hs3st1 hs3st1l1 Id4 IPIP27A jarid2a lhx1a lrrtm1 mak mapk14a max mchr1a mef2aa meis2a meis4.1a mrc1a nr5a2 nup155 NUPL2 ovol1 oxtrl park2 pcolce2b pink1 Popdc2 Popdc3 prothymosinalphaa prrx1b PurinergicreceptorY2 rassf7b scrt2 sema6dl Semaphorin6bb si:ch211-120j21.1 slc50a1 snrnp35 snrnp48 sox1a Sox2 Tac3b taok2b tcof tet2(ENSDART00000113020) tet3(ENSDART00000137355) tfe3a tfe3b tnfb TRABD2A TTC19 Vangl1 vasa Vrk2 ywhai zmynd11
Re: Announcement of FOURTH Solicitation for NIH-funded Resource to Target Zebrafish Genes with Engineered Nucleases
Author: Keith Joung
Date: Mon, 04 Mar 2013 02:14
Date: Mon, 04 Mar 2013 02:14
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Dear all, I'm pleased to announce that we have now completed construction of sequence-verified plasmids encoding TALEN pairs for all 96 endogenous zebrafish genes targeted in our FOURTH NIH-sponsored solicitation. These plasmids will be deposited tomorrow with Addgene and should become available in the next few weeks (and will be available here: http://www.addgene.org/talengineering/TALENzebrafish/). You can also e-mail Jason Niehaus from Addgene (jason@addgene.org) if you wish to be notified when a particular pair becomes available. With best regards, Keith Joung Randy Peterson Joanna Yeh Jon Foley Deepak Reyon Jeff Sander
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