{"text_format":"2","workbook":"xlsx","n_sheets":3,"sheets":["investigation","study_assays","datamatrix"],"not_rendered":{"charts":0,"images":0,"macros":0,"external_links":0,"defined_names":0,"comments":1,"pivot_tables":0},"unopened":[],"bounds":{"document_bytes":16777216,"sheet_cells":100000,"run_cost":"one","rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0,"cell_chars":16384,"cell_head_chars":4096},"cells_cut":0,"cells_raw":0,"read":"whole","date_system":"1900"}

{"sheet":"investigation","index":0,"n_rows":91,"n_cols":5,"rows_kept":91,"cut":false,"hidden":false,"merged":[]}
["ONTOLOGY SOURCE REFERENCE"]
["Term Source Name","OBI","CHEBI","UO"]
["Term Source File"]
["Term Source Version","v 1.26","v 1.26","v 1.26"]
["Term Source Description","Ontology for Biomedical Investigations","Chemical Entity of Biological Interest","Unit Ontology"]
["INVESTIGATION"]
["Investigation Identifier"]
["Investigation Title"]
["Investigation Description"]
["Investigation Submission Date"]
["Investigation Public Release Date"]
["INVESTIGATION PUBLICATIONS"]
["Investigation PubMed ID"]
["Investigation Publication DOI"]
["Investigation Publication Author list"]
["Investigation Publication Title"]
["Investigation Publication Status"]
["Investigation Publication Status Term Accession Number"]
["Investigation Publication Status Term Source REF"]
["INVESTIGATION CONTACTS"]
["Investigation Person Last Name"]
["Investigation Person First Name"]
["Investigation Person Mid Initials"]
["Investigation Person Email"]
["Investigation Person Phone"]
["Investigation Person Fax"]
["Investigation Person Address"]
["Investigation Person Affiliation"]
["Investigation Person Roles"]
["Investigation Person Roles Term Accession Number"]
["Investigation Person Roles Term Source REF"]
["STUDY"]
["Study Identifier"]
["Study Title","RB1 SNRNASM"]
["Study Submission Date"]
["Study Public Release Date"]
["Study Description","The WT RB1 5′ UTR sequence with hairpin adapters for SHAPE (GGCCTTCGGGCCAAGCTCAGTTGCCGGGCGGGGGAGGGCGCGTCCGGTTTTTCTCAGGGGACGTTGAAATTATTTTTGTAACGGGAGTCGGGAGAGGACGGGGCGTGCCCCGACGTGCGCGCGCGTCGTCCTCCCCGGCGCTCCTCCACAGCTCGCTGGCTCCCGCCGCGGAAAGGCGTCATGCCGTCGATCCGGTTCGCCGGATCCAAATCGGGCTTCGGTCCGGTTC) was inserted between the SgfI and MluI sites of the pCMV6-AC nontagged precision shuttle vector (Origene). Hairpin adapters are indicated in bold.  The mutant sequences, which varied only by point mutations, were inserted into pUC57 by Genscript.  The Bos taurus RB1(GGCCTTCGGGCCAACGCGGCGCTCGGTTGCCGGGCGAGGGAGGGCCGGCCCGGTTTTTTTCTCAGGGGAACGTTCAAATTATTTTTGTAACGGGAGTCGGCCGAGGACGGGGCGTGCCCGAGGTGCGCGCGTCCTCTCCCTTCCCCGGCCCTCCTCCAGCGCCCGCCGGCGCCTGCCCAGCGAGCGCGTCATGCCGTCGATCCGGTTCGCCGGATCCAAATCGGGCTTCGGTCCGGTTC) and T.m. laitorostris RB1 (GGCCTTCGGGCCAAGCTCGGTTGCCGGGTGGGGAGGGCTTGTCCGGTTTTTCTCAGGGGACGTTCAAATTATTTTTGTAACGGGAGTCGAGAGAGGACGGGGCGTGCCCCGACGTGTGCGCGCGTCCCCCGCCCCCGCCCTCCTCCACAGCTCTCTAGCTCCTACCCTGTAAGGGCGTCATGCCGTCGATCCGGTTCGCCGGATCCAAATCGGGCTTCGGTCCGGTTC) sequences were also cloned by Genscript into pUC57.  A T7 promoter (TAATACGACTCACTATAGGG) was introduced to the 5′ end of the 5′ UTR during PCR amplification followed by transcription with the T7 high yield RNA synthesis kit (New England Biolabs) and cleanup by MegaClear (Ambion). Selective 2′-Hydroxyl Acylation and Primer Extension (SHAPE) experiments were performed as previously described (Martin et al. 2012) with a few modifications. 2 pmol RNA were used for each reaction and, after denaturation as previously described, were folded in a final concentration of 100 mM HEPES, pH 8.0, 10 mM MgCl2, 100 mM KCl at 37°C for 15 min. Primer extension was performed as previously described, but with 2 pmol of Vic or Ned-labeled primer without RNase inhibitor.  The samples with and without NMIA were reverse transcribed with the Vic-labeled primer; the Ned-labeled primer was used to make sequencing ladders using unreacted RNA and 1 ul 5 mM ddGTP, ddCTP, ddATP or ddTTP.  The base and neutralization steps used to degrade remaining RNA in the cDNA samples were found to be unnecessary and were eliminated in later experiments. The cDNA pellets were dried, resuspended in Hi-Di formamide (Applied Biosystems/Life Technologies), and run on an Applied Biosystems 3500 Genetic Analyzer.  The resulting data were analyzed using QuSHAPE (Karabiber et al. 2013)\n\n"]
["Study File Name"]
["STUDY DESIGN DESCRIPTORS"]
["Study Design Type","SNRNASM"]
["Study Design Type Term Accession Number","OBI"]
["Study Design Type Term Source REF"]
["STUDY PUBLICATIONS"]
["Study PubMed ID"]
["Study Publication DOI"]
["Study Publication Author list","Katrina M Kutchko, Wes Sanders, Amanda Solem, Matthew Halvorsen, Ben Ziehr, Nathaniel Moorman, and Alain Laederach"]
["Study Publication Title"]
["Study Publication Status","In preparation"]
["Study Publication Status Term Accession Number"]
["Study Publication Status Term Source REF","OBI"]
["STUDY FACTORS"]
["Study Factor Name"]
["Study Factor Type"]
["Study Factor Type Term Accession Number"]
["Study Factor Type Term Source REF","CHEBI",null,"CHEBI"]
["STUDY ASSAYS"]
["Study Assay Measurement Type","single nucleotide resolution mapping structure"]
["Study Assay Measurement Type Term Accession Number"]
["Study Assay Measurement Type Term Source REF","OBI"]
["Study Assay Technology Type","capillary electrophoresis"]
["Study Assay Technology Type Term Accession Number"]
["Study Assay Technology Type Term Source REF"]
["Study Assay Technology Platform"]
["Study Assay File Name"]
["STUDY PROTOCOLS"]
["Study Protocol Name","1M7 Structure Mapping"]
["Study Protocol Type"]
["Study Protocol Type Term Accession Number"]
["Study Protocol Type Term Source REF","OBI","OBI","OBI"]
["Study Protocol Description"]
["Study Protocol URI"]
["Study Protocol Version"]
["Study Protocol Parameters Name"]
["Study Protocol Parameters Name Term Accession Number"]
["Study Protocol Parameters Name Term Source REF"]
["Study Protocol Components Name"]
["Study Protocol Components Type"]
["Study Protocol Components Type Term Accession Number"]
["Study Protocol Components Type Term Source REF"]
["STUDY CONTACTS"]
["Study Person Last Name","Laederach","Kutchko","Sanders","Solem"]
["Study Person First Name","Alain","Katrina","Wes","Amanda"]
["Study Person Mid Initials",null,"M"]
["Study Person Email","alain@unc.edu","kutchko@email.unc.edu","wessanders99@gmail.com","amanda.solem@gmail.com"]
["Study Person Phone"]
["Study Person Fax"]
["Study Person Address"]
["Study Person Affiliation","University of North Carolina at Chapel Hill","University of North Carolina at Chapel Hill","University of North Carolina at Chapel Hill","University of North Carolina at Chapel Hill"]
["Study Person Roles","Principal Investigator","Graduate Student","Lab Technician","Postdoctoral Fellow"]
["Study Person Roles Term Accession Number"]
["Study Person Roles Term Source REF","OBI","OBI","OBI"]

{"sheet":"study_assays","index":1,"n_rows":17,"n_cols":15,"rows_kept":17,"cut":false,"hidden":false,"merged":[]}
["Source Name","Characteristics[Nucleotide Sequence]","Characteristics[Nucleotide Type]","Characteristics[RNA Production]","Protocol REF","Parameter Value[Data Starts at Sequence Position]","Parameter Value[software]","Assay Name","Raw Data File","Data Starts At","Performer","Date","Factor Value[probing agent]","Factor Value[folding salt]","Factor Value[folding salt concentration]"]
["WT_Mean","GCUCAGUUGCCGGGCGGGGGAGGGCGCGUCCGGUUUUUCUCAGGGGACGUUGAAAUUAUUUUUGUAACGGGAGUCGGGAGAGGACGGGGCGUGCCCCGACGUGCGCGCGCGUCGUCCUCCCCGGCGCUCCUCCACAGCUCGCUGGCUCCCGCCGCGGAAAGGCGUC","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["WT_SD","GCUCAGUUGCCGGGCGGGGGAGGGCGCGUCCGGUUUUUCUCAGGGGACGUUGAAAUUAUUUUUGUAACGGGAGUCGGGAGAGGACGGGGCGUGCCCCGACGUGCGCGCGCGUCGUCCUCCCCGGCGCUCCUCCACAGCUCGCUGGCUCCCGCCGCGGAAAGGCGUC","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["C4A_Mean","GCUAAGUUGCCGGGCGGGGGAGGGCGCGUCCGGUUUUUCUCAGGGGACGUUGAAAUUAUUUUUGUAACGGGAGUCGGGAGAGGACGGGGCGUGCCCCGACGUGCGCGCGCGUCGUCCUCCCCGGCGCUCCUCCACAGCUCGCUGGCUCCCGCCGCGGAAAGGCGUC","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["C4A_SD","GCUAAGUUGCCGGGCGGGGGAGGGCGCGUCCGGUUUUUCUCAGGGGACGUUGAAAUUAUUUUUGUAACGGGAGUCGGGAGAGGACGGGGCGUGCCCCGACGUGCGCGCGCGUCGUCCUCCCCGGCGCUCCUCCACAGCUCGCUGGCUCCCGCCGCGGAAAGGCGUC","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["C15U_Mean","GCUCAGUUGCCGGGUGGGGGAGGGCGCGUCCGGUUUUUCUCAGGGGACGUUGAAAUUAUUUUUGUAACGGGAGUCGGGAGAGGACGGGGCGUGCCCCGACGUGCGCGCGCGUCGUCCUCCCCGGCGCUCCUCCACAGCUCGCUGGCUCCCGCCGCGGAAAGGCGUC","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["C15U_SD","GCUCAGUUGCCGGGUGGGGGAGGGCGCGUCCGGUUUUUCUCAGGGGACGUUGAAAUUAUUUUUGUAACGGGAGUCGGGAGAGGACGGGGCGUGCCCCGACGUGCGCGCGCGUCGUCCUCCCCGGCGCUCCUCCACAGCUCGCUGGCUCCCGCCGCGGAAAGGCGUC","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["G17C_Mean","GCUCAGUUGCCGGGCGCGGGAGGGCGCGUCCGGUUUUUCUCAGGGGACGUUGAAAUUAUUUUUGUAACGGGAGUCGGGAGAGGACGGGGCGUGCCCCGACGUGCGCGCGCGUCGUCCUCCCCGGCGCUCCUCCACAGCUCGCUGGCUCCCGCCGCGGAAAGGCGUC","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["G17C_SD","GCUCAGUUGCCGGGCGCGGGAGGGCGCGUCCGGUUUUUCUCAGGGGACGUUGAAAUUAUUUUUGUAACGGGAGUCGGGAGAGGACGGGGCGUGCCCCGACGUGCGCGCGCGUCGUCCUCCCCGGCGCUCCUCCACAGCUCGCUGGCUCCCGCCGCGGAAAGGCGUC","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["G18U_Mean","GCUCAGUUGCCGGGCGGUGGAGGGCGCGUCCGGUUUUUCUCAGGGGACGUUGAAAUUAUUUUUGUAACGGGAGUCGGGAGAGGACGGGGCGUGCCCCGACGUGCGCGCGCGUCGUCCUCCCCGGCGCUCCUCCACAGCUCGCUGGCUCCCGCCGCGGAAAGGCGUC","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["G18U_SD","GCUCAGUUGCCGGGCGGUGGAGGGCGCGUCCGGUUUUUCUCAGGGGACGUUGAAAUUAUUUUUGUAACGGGAGUCGGGAGAGGACGGGGCGUGCCCCGACGUGCGCGCGCGUCGUCCUCCCCGGCGCUCCUCCACAGCUCGCUGGCUCCCGCCGCGGAAAGGCGUC","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["C166U_Mean","GCUCAGUUGCCGGGCGGGGGAGGGCGCGUCCGGUUUUUCUCAGGGGACGUUGAAAUUAUUUUUGUAACGGGAGUCGGGAGAGGACGGGGCGUGCCCCGACGUGCGCGCGCGUCGUCCUCCCCGGCGCUCCUCCACAGCUCGCUGGCUCCCGCCGCGGAAAGGCGUU","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["C166U_SD","GCUCAGUUGCCGGGCGGGGGAGGGCGCGUCCGGUUUUUCUCAGGGGACGUUGAAAUUAUUUUUGUAACGGGAGUCGGGAGAGGACGGGGCGUGCCCCGACGUGCGCGCGCGUCGUCCUCCCCGGCGCUCCUCCACAGCUCGCUGGCUCCCGCCGCGGAAAGGCGUU","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["BTaurus_Mean","CGCGGCGCUCGGUUGCCGGGCGAGGGAGGGCCGGCCCGGUUUUUUUCUCAGGGGAACGUUCAAAUUAUUUUUGUAACGGGAGUCGGCCGAGGACGGGGCGUGCCCGAGGUGCGCGCGUCCUCUCCCUUCCCCGGCCCUCCUCCAGCGCCCGCCGGCGCCUGCCCAGCGAGCGCGUC","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["BTaurus_SD","CGCGGCGCUCGGUUGCCGGGCGAGGGAGGGCCGGCCCGGUUUUUUUCUCAGGGGAACGUUCAAAUUAUUUUUGUAACGGGAGUCGGCCGAGGACGGGGCGUGCCCGAGGUGCGCGCGUCCUCUCCCUUCCCCGGCCCUCCUCCAGCGCCCGCCGGCGCCUGCCCAGCGAGCGCGUC","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["TMLatirostris_Mean","GCUCGGUUGCCGGGUGGGGAGGGCUUGUCCGGUUUUUCUCAGGGGACGUUCAAAUUAUUUUUGUAACGGGAGUCGAGAGAGGACGGGGCGUGCCCCGACGUGUGCGCGCGUCCCCCGCCCCCGCCCUCCUCCACAGCUCUCUAGCUCCUACCCUGUAAGGGCGUC","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]
["TMLatirostris_SD","GCUCGGUUGCCGGGUGGGGAGGGCUUGUCCGGUUUUUCUCAGGGGACGUUCAAAUUAUUUUUGUAACGGGAGUCGAGAGAGGACGGGGCGUGCCCCGACGUGUGCGCGCGUCCCCCGCCCCCGCCCUCCUCCACAGCUCUCUAGCUCCUACCCUGUAAGGGCGUC","RNA","in vitro synthesis","NMIA RNA structure mapping assay",1,{"$nulls":4},"Katrina Kutchko","2014-11-29"]

{"sheet":"datamatrix","index":2,"n_rows":167,"n_cols":16,"rows_kept":167,"cut":false,"hidden":false,"merged":[]}
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