{"text_format":"1","workbook":"xlsx","n_sheets":5,"sheets":["IDF","SDRF","IDF_example","SDRF_example","restore_SDRF"],"not_rendered":{"charts":0,"images":0,"macros":1,"external_links":1,"defined_names":83,"comments":0,"pivot_tables":0},"unopened":[],"bounds":{"document_bytes":16777216,"sheet_cells":100000,"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":"IDF","index":0,"n_rows":159,"n_cols":11,"rows_kept":159,"cut":false,"hidden":false,"merged":[[4,1,4,3],[6,1,6,3],[68,0,68,1],[49,3,49,8],[2,0,2,1]]}
["# Template submission sheet for FungiNet RNA-Seq experiments  (yellow and green cells are mandatory)",null,"used Lookup Table Version:","V2.2_20190709"]
["[IDF] Investigation Description File"]
["For further information, please read Description_Templates_V2.2.doc"]
["# This section contains the top-level information for your experiment"]
["Investigation Title"]
["Experiment Class",{"$f":"IF(IDF!B5=\"\",\"\",\"RNA-seq\")","v":""}]
["Experiment Description"]
["Experimental Design"]
["Experimental Design Term Source REF",{"$f":"IF(B8=\"\",\"\",\"MGED Ontology\")","v":""}]
["FungiNet Project"]
[]
["# 'Experimental Factors' used to describe the variables investigated by your experiment"]
["Experimental Factor Name"]
["Experimental Factor Type"]
["Experimental Factor Term Source REF",{"$f":"IF(B14=\"\",\"\",\"MGED Ontology\")","v":""},{"$f":"IF(C14=\"\",\"\",\"MGED Ontology\")","v":""},{"$f":"IF(D14=\"\",\"\",\"MGED Ontology\")","v":""},{"$f":"IF(E14=\"\",\"\",\"MGED Ontology\")","v":""},{"$f":"IF(F14=\"\",\"\",\"MGED Ontology\")","v":""},{"$f":"IF(#REF!=\"\",\"\",\"MGED Ontology\")","v":{"$error":"#REF!"}},{"$f":"IF(#REF!=\"\",\"\",\"MGED Ontology\")","v":{"$error":"#REF!"}}]
[]
["# Quality control information"]
["Quality Control Type"]
["Quality Control Term Source REF",{"$f":"IF(B18=\"\",\"\",\"MGED Ontology\")","v":""},{"$f":"IF(C18=\"\",\"\",\"MGED Ontology\")","v":""},{"$f":"IF(D18=\"\",\"\",\"MGED Ontology\")","v":""}]
[]
["# Data release information"]
["Public Release Date"]
["Database"]
["Accession Number"]
[]
["# Personal information about the data submitter(s) and investigator(s)"]
["Person Last Name"]
["Person First Name"]
["Person Mid Initials"]
["Person Email"]
["Person Phone"]
["Person Address"]
["Person Affiliation - Institution"]
["Person Affiliation - Department"]
["Person Roles"]
[]
["Cooperation partners within FungiNet - Institution"]
["Cooperation partners within FungiNet - Department"]
["Cooperation partners within SysMoDB"]
["Other cooperation partners"]
[]
["# Publications based on the data described in this file"]
["PubMed ID"]
["Publication DOI or Journal/Book Title"]
["Publication Author List"]
["Publication Title"]
["Publication Status"]
[]
["# Protocols (Standard Operation Procedures, SOPs)  - new protocols may only be added by the infrastructure team"]
["#","Extraction Protocols","Sequencing Protocols","Data Processing Protocols",null,null,null,null,null,"Storage Protocols"]
["Protocol Name","RNA EXTRACTION","SEQUENCING","QUALITY CONTROL OF RAW DATA","QUALITY TRIMMING OF RAW DATA","MAPPING","COUNTING","DIFFERENTIAL EXPRESSION FILTERING","ANNOTATION","STORAGE","NO STORAGE"]
["Protocol URI","rna_extraction","sequencing","qc_raw","qt_raw","mapping","counting","filtering","annotation","storage","no_storage"]
["Protocol Type","nucleic_acid_extraction","unknown_protocol_type","unknown_protocol_type","unknown_protocol_type","unknown_protocol_type","unknown_protocol_type","unknown_protocol_type","unknown_protocol_type","store","store"]
["Protocol Term Source REF","MGED Ontology","MGED Ontology","MGED Ontology",null,null,null,null,null,"MGED Ontology","MGED Ontology"]
["Protocol Description","details of RNA extraction from the biological sample","details of the sequencing process","first step of data processing","second step of data processing","third step of data processing","fourth step of data processing","details of filtering for differentially regulated genes","genome, functional and structural annotation of all genes in the dataset","storage of data ","no storage of data"]
["Protocol Parameters","260/280;230/280;RIN/RNA integrity number;Concentration;Volume;Extraction kit","Performer;Technology Type;Read Length;Library Source; Library Strategy;Library Selection; Library Layout",null,null,null,null,null,"Source, Version and Date of Annotation"]
["Protocol Hardware"]
["Protocol Software",null,null,"FastQC","trimmomatic","HiSat2","featureCounts","DESeq; DESeq2; edgeR; Limma"]
[]
["# Controlled vocabulary sources - new sources may only be added by the data management team"]
["Term Source Name","MGED Ontology"]
["Term Source File","http://mged.sourceforge.net/ontologies/MGEDontology.php"]
["Term Source Version","1.3.1.1"]
[]
["# Filename of the 'SDRF' part belonging to this 'IDF' part"]
["SDRF File",{"$f":"MID(CELL(\"Dateiname\"),SEARCH(\"[\",CELL(\"Dateiname\"))+1,SEARCH(\"]\",CELL(\"Dateiname\"))-SEARCH(\"[\",CELL(\"Dateiname\"))-1)","v":"FungiNet_template_RNA-seq_V2.2.xlsm"}]
[]
["# Default values for data transfer into the SDRF sheet (Macros must be activated)"]
[]
["# Default Sample Material Type"]
["# Default Organism"]
["# Default Strain or Line"]
["# Default Organism Part"]
["# Default Organism Status"]
["# Default Number of fungal cells"]
["# Default Unit for number of fungal cells"]
["# Default Sex"]
["# Default Age"]
["# Default Age Time Unit"]
["# Default Sampling Time Point"]
["# Default Sampling Time Point Unit"]
["# Default Temperature in °C"]
["# Default Temperature Unit"]
["# Default pH"]
["# Default Atmosphere"]
["# Default Compound"]
["# Default Medium"]
["# Default Nutrient"]
["# Default Biobank Storage Protocol"]
["# Default Biobank Storage Date"]
["# Default Biobank Storage Location"]
["# Default RNA Extraction Protocol",{"$f":"IF(IDF!$B$71=\"\",\"\",IDF!$B$51)","v":""}]
[]
["# Default 260/280 Ratio"]
["# Default 230/280 Ratio"]
["# Default RIN/ RNA integrity number"]
["# Default RNA Concentration"]
["# Default RNA Concentration Unit"]
["# Default RNA Volume"]
["# Default RNA Volume Unit"]
["# Default RNA Extraction Kit"]
["# Default RNA Material Type",{"$f":"IF($B$92=\"\",\"\",\"total_RNA\")","v":""}]
["# Default RNA Extraction Date"]
["# Default RNA Storage Protocol"]
["# Default RNA Storage Date"]
["# Default RNA Storage Location"]
["# Default Sequencing Protocol",{"$f":"IF(IDF!$B$71=\"\",\"\",IDF!$C$51)","v":""}]
[]
["# Default Sequencing Performer"]
["# Default Sequencing Technology Type"]
["# Default Sequencing Read Length"]
["# Default Sequencing Instrument"]
["# Default Sequencing Library Source"]
["# Default Sequencing Library Strategy"]
["# Default Sequencing Library Selection"]
["# Default Sequencing Library Layout"]
["# Default Sequencing Date"]
["# Default Sequencing Storage Protocol",{"$f":"IF(B107=\"\",\"\",\"STORAGE\")","v":""}]
["# Default Sequencing Storage Date"]
["# Default Sequencing Storage Location - Server",{"$f":"IF(B107=\"\",\"\",\"stored at HKI Jena\")","v":""}]
["# Default Sequencing Storage Location - Folder"]
[]
["# Default Data Processing Protocol",{"$f":"IF(D58=\"\",\"\",IF(B107=\"\",\"\",D51))","v":""}]
["# Default Data Processing Software",{"$f":"IF(D58=\"\",\"\",IF(B107=\"\",\"\",D58))","v":""}]
["# Default Data Processing Protocol Parameters and Values"]
[]
["# Default Data Processing Protocol",{"$f":"IF(E58=\"\",\"\",IF(B107=\"\",\"\",E51))","v":""}]
["# Default Data Processing Software",{"$f":"IF(E58=\"\",\"\",IF(B107=\"\",\"\",E58))","v":""}]
["# Default Data Processing Protocol Parameters and Values"]
[]
["# Default Data Processing Protocol",{"$f":"IF(F58=\"\",\"\",IF(B107=\"\",\"\",F51))","v":""}]
["# Default Data Processing Software",{"$f":"IF(F58=\"\",\"\",IF(B107=\"\",\"\",F58))","v":""}]
["# Default Data Processing Protocol Parameters and Values"]
[]
["# Default Data Processing Protocol",{"$f":"IF(G58=\"\",\"\",IF(B107=\"\",\"\",G51))","v":""}]
["# Default Data Processing Software",{"$f":"IF(G58=\"\",\"\",IF(B107=\"\",\"\",G58))","v":""}]
["# Default Data Processing Protocol Parameters and Values"]
[]
["# Default Data Processing Protocol",{"$f":"IF(H58=\"\",\"\",IF(B107=\"\",\"\",H51))","v":""}]
["# Default Data Processing Software",{"$f":"IF(H58=\"\",\"\",IF(B107=\"\",\"\",H58))","v":""}]
["# Default Data Processing Protocol Parameters and Values"]
[]
["# Default Data Processing Protocol",{"$f":"IF($B92=\"\",\"\",\"ANNOTATION\")","v":""}]
["# Default Genome Annotation Source"]
["# Default Genome Annotation Version"]
["# Default Genome Annotation Date"]
["# Default Genome Annotation Data File"]
["# Default Structural Annotation Source"]
["# Default Structural Annotation Version"]
["# Default Structural Annotation Date"]
["# Default Structural Annotation Data File"]
["# Default Functional Annotation Source"]
["# Default Functional Annotation Version"]
["# Default Functional Annotation Date"]
["# Default Functional Annotation Data File"]
["# Default Data Processing Storage Protocol",{"$f":"IF(B107=\"\",\"\",\"STORAGE\")","v":""}]
["# Default Data Processing Storage Date"]
["# Default Data Processing Storage Location - Server",{"$f":"IF(B107=\"\",\"\",\"stored at HKI Jena: /sbiarchiv\")","v":""}]
["# Default Data Processing Storage Location - Folder"]

{"sheet":"SDRF","index":1,"n_rows":1999,"n_cols":99,"rows_kept":562,"cut":true,"hidden":false,"merged":[[5,98,5,100],[5,92,5,96],[5,54,5,91],[0,0,0,2],[5,38,5,53],[1,0,1,1],[5,0,5,22],[5,23,5,37],[2,0,2,2]],"bounds":{"rows_first":250,"rows_last":62,"rows_between":250,"halvings":3}}
["# Template submission sheet for FungiNet RNA-Seq experiments"]
["[SDRF] Sample and Data Relationship File"]
["# Please fill in as much columns as possible, yellow and green cells are mandatory"]
["s",2,3,4,5,6,null,null,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,null,51,52,53,54,null,55,56,57,null,58,59,60,null,61,62,63,null,64,65,66,67,null,69,70,71,72,null,null,null,null,null,null,null,null,73,74,75,null,76,77,78,79,80,81,82]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"IF(IDF!$B$14=\"age\",IF($J5=\"\",\"\",$J5),IF(IDF!$B$14=\"atmosphere\",IF($Q5=\"\",\"\",$Q5),IF(IDF!$B$14=\"organism\",IF($C5=\"\",\"\",$C5),IF(IDF!$B$14=\"organism_part\",IF($E5=\"\",\"\",$E5),IF(IDF!$B$14=\"sampling_time_point\",IF($L5=\"\",\"\",$L5),IF(IDF!$B$14=\"temperature\",IF($N5=\"\",\"\",$N5),IF(IDF!$B$14=\"pH\",IF($P5=\"\",\"\",$P5),IF(IDF!$B$14=\"compound\",IF($R5=\"\",\"\",$R5),IF(IDF!$B$14=\"media\",IF($S5=\"\",\"\",$S5),IF(IDF!$B$14=\"nutrients\",IF($T5=\"\",\"\",$T5),IF(IDF!$B$14=\"strain_or_line\",IF($D5=\"\",\"\",$D5),\"\")))))))))))","v":""},{"$f":"IF(IDF!$C$14=\"age\",IF($J5=\"\",\"\",$J5),IF(IDF!$C$14=\"atmosphere\",IF($Q5=\"\",\"\",$Q5),IF(IDF!$C$14=\"organism\",IF($C5=\"\",\"\",$C5),IF(IDF!$C$14=\"organism_part\",IF($E5=\"\",\"\",$E5),IF(IDF!$C$14=\"sampling_time_point\",IF($L5=\"\",\"\",$L5),IF(IDF!$C$14=\"temperature\",IF($N5=\"\",\"\",$N5),IF(IDF!$C$14=\"pH\",IF($P5=\"\",\"\",$P5),IF(IDF!$C$14=\"compound\",IF($R5=\"\",\"\",$R5),IF(IDF!$C$14=\"media\",IF($S5=\"\",\"\",$S5),IF(IDF!$C$14=\"nutrients\",IF($T5=\"\",\"\",$T5),IF(IDF!$C$14=\"strain_or_line\",IF($D5=\"\",\"\",$D5),\"\")))))))))))","v":""},null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"IF(IDF!$D$14=\"age\",IF($J5=\"\",\"\",$J5),IF(IDF!$D$14=\"atmosphere\",IF($Q5=\"\",\"\",$Q5),IF(IDF!$D$14=\"organism\",IF($C5=\"\",\"\",$C5),IF(IDF!$D$14=\"organism_part\",IF($E5=\"\",\"\",$E5),IF(IDF!$D$14=\"sampling_time_point\",IF($L5=\"\",\"\",$L5),IF(IDF!$D$14=\"temperature\",IF($N5=\"\",\"\",$N5),IF(IDF!$D$14=\"pH\",IF($P5=\"\",\"\",$P5),IF(IDF!$D$14=\"compound\",IF($R5=\"\",\"\",$R5),IF(IDF!$D$14=\"media\",IF($S5=\"\",\"\",$S5),IF(IDF!$D$14=\"nutrients\",IF($T5=\"\",\"\",$T5),IF(IDF!$D$14=\"strain_or_line\",IF($D5=\"\",\"\",$D5),\"\")))))))))))","v":""},{"$f":"IF(IDF!$E$14=\"age\",IF($J5=\"\",\"\",$J5),IF(IDF!$E$14=\"atmosphere\",IF($Q5=\"\",\"\",$Q5),IF(IDF!$E$14=\"organism\",IF($C5=\"\",\"\",$C5),IF(IDF!$E$14=\"organism_part\",IF($E5=\"\",\"\",$E5),IF(IDF!$E$14=\"sampling_time_point\",IF($L5=\"\",\"\",$L5),IF(IDF!$E$14=\"temperature\",IF($N5=\"\",\"\",$N5),IF(IDF!$E$14=\"pH\",IF($P5=\"\",\"\",$P5),IF(IDF!$E$14=\"compound\",IF($R5=\"\",\"\",$R5),IF(IDF!$E$14=\"media\",IF($S5=\"\",\"\",$S5),IF(IDF!$E$14=\"nutrients\",IF($T5=\"\",\"\",$T5),IF(IDF!$E$14=\"strain_or_line\",IF($D5=\"\",\"\",$D5),\"\")))))))))))","v":""},{"$f":"IF(IDF!$F$14=\"age\",IF($J5=\"\",\"\",$J5),IF(IDF!$F$14=\"atmosphere\",IF($Q5=\"\",\"\",$Q5),IF(IDF!$F$14=\"organism\",IF($C5=\"\",\"\",$C5),IF(IDF!$F$14=\"organism_part\",IF($E5=\"\",\"\",$E5),IF(IDF!$F$14=\"sampling_time_point\",IF($L5=\"\",\"\",$L5),IF(IDF!$F$14=\"temperature\",IF($N5=\"\",\"\",$N5),IF(IDF!$F$14=\"pH\",IF($P5=\"\",\"\",$P5),IF(IDF!$F$14=\"compound\",IF($R5=\"\",\"\",$R5),IF(IDF!$F$14=\"media\",IF($S5=\"\",\"\",$S5),IF(IDF!$F$14=\"nutrients\",IF($T5=\"\",\"\",$T5),IF(IDF!$F$14=\"strain_or_line\",IF($D5=\"\",\"\",$D5),\"\")))))))))))","v":""},null,{"$f":"IF($A5=\"\",\"\",\"MGED Ontology\")","v":""}]
["# Source",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"RNA Extraction",null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Sequencing",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Data Processing",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Experimental Factor Values",null,null,null,null,"Term Source","Fold Change Assignment"]
["# Specimen","Material Type","Organism","Strain or Line","Organism Part","OrganismStatus","Number of fungal cells","Unit for number of fungal cells","Sex","Age","Age Time Unit","Sampling Time Point","Sampling Time Point Unit","Temperature in °C","Temperature Unit","pH","Atmosphere","Compound","Media","Nutrients","Storage Protocol","Storage Date","Storage Location","Extraction Protocol","Extract Name","260/280","230/280","RIN / RNA integrity number","Concentration","Concentration Unit","Volume","Volume Unit","Extraction Kit","Material Type","Extraction Date","Storage Protocol","Storage Date","Storage Location","Sequencing Protocol","Assay Name","Sequencing Performer","Technology Type","Read Length","Sequencing Instrument","Library Source","Library Strategy","Library Selection","Library Layout","Sequencing Date","Storage Protocol","Storage Date","Storage Location - Server","Storage Location - Folder","Data File","Data Processing Protocol","Data Processing Software","Parameters And Values","Description","Data Processing Protocol","Data Processing Software","Parameters And Values","Description","Data Processing Protocol","Data Processing Software","Parameters And Values","Description","Data Processing Protocol","Data Processing Software","Parameters And Values","Description","Data Processing Protocol","Data Processing Software","Parameters And Values","Description","Data Processing Protocol","Genome Annotation Source","Genome Annotation Version","Genome Annotation Date","Genome Annotation Data File","Structural Annotation Source","Structural Annotation Version","Structural Annotation Date","Structural Annotation Data File","Functional Annotation Source","Functional Annotation Version","Functional Annotation Date","Functional Annotation Data File","Storage Protocol","Storage Date","Storage Location - Server","Storage Location - Folder","Derived Data File",{"$f":"IF(IDF!B$13=\"\",\"\",IDF!$B13)","v":""},{"$f":"IF(IDF!C$13=\"\",\"\",IDF!C$13)","v":""},{"$f":"IF(IDF!D$13=\"\",\"\",IDF!D$13)","v":""},{"$f":"IF(IDF!E$13=\"\",\"\",IDF!E$13)","v":""},{"$f":"IF(IDF!F$13=\"\",\"\",IDF!F$13)","v":""},"Term Source"]
["Source Name","Material Type","Characteristics[Organism]","Characteristics[StrainOrLine]","Characteristics[OrganismPart]","Characteristics[OrganismStatus]","Characteristics[Number of fungal organisms]","Unit[CellUnit]","Characteristics[Sex]","Characteristics[Age]","Unit[TimeUnit]","Characteristics[SamplingTimePoint]","Unit[TimeUnit]","Characteristics[Temperature]","Unit[TemperatureUnit]","Characteristics[pH]","Characteristics[Atmosphere]","Characteristics[Compound]","Characteristics[Media]","Characteristics[Nutrients]","Protocol REF","Date","Comment","Protocol REF","Extract Name","Parameter[260/280]","Parameter[230/280]","Parameter[RIN/RNA integrity number]","Parameter[Concentration]","Unit[ConcentrationUnit]","Parameter[Volume]","Unit[VolumeUnit]","Parameter[Kit]","Material Type","Date","Protocol REF","Date","Comment","Protocol REF","Assay Name","Parameter[Performer]","Parameter[Technology Type]","Parameter[Read Length]","Protocol Hardware","Parameter[Library_Source]","Parameter[Library_Strategy]","Parameter[Library_Selection]","Parameter[Library_Layout]","Date","Protocol REF","Date","Comment",null,"Array Data File","Protocol REF","Protocol Software","Comment[Parameters]","Description","Protocol REF","Protocol Software","Comment[Parameters]","Description","Protocol REF","Protocol Software","Comment[Parameters]","Description","Protocol REF","Protocol Software","Comment[Parameters]","Description","Protocol REF","Protocol Software","Comment[Parameters]","Description","Protocol REF","Comment[Annot_Source]","Comment[Annot_Version]","Date","Comment[Annot_File]","Comment[Annot_Source]","Comment[Annot_Version]","Date","Comment[Annot_File]","Comment[Annot_Source]","Comment[Annot_Version]","Date","Comment[Annot_File]","Protocol REF","Date","Comment",null,"Derived Array Data Matrix File",{"$f":"\"Factor Value[\"&CO7&\"]\"","v":"Factor Value[]"},{"$f":"\"Factor Value[\"&CP7&\"]\"","v":"Factor Value[]"},{"$f":"\"Factor Value[\"&CQ7&\"]\"","v":"Factor Value[]"},{"$f":"\"Factor Value[\"&CR7&\"]\"","v":"Factor Value[]"},{"$f":"\"Factor Value[\"&CS7&\"]\"","v":"Factor Value[]"},"Term Source REF"]
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{"sheet":"IDF_example","index":2,"n_rows":152,"n_cols":11,"rows_kept":152,"cut":false,"hidden":false,"merged":[[4,1,4,3],[6,1,6,3],[49,3,49,8],[68,0,68,1]]}
["# Template submission sheet for FungiNet RNA-Seq experiments - Example",null,"used Lookup Table Version:","V1.9.4_20150827"]
["[IDF] Investigation Description File"]
["S"]
["# This section contains the top-level information for your experiment"]
["Investigation Title","Defining the transcriptional landscape of Candida glabrata by RNA-Seq."]
["Experiment Class",{"$f":"IF(IDF_example!B5=\"\",\"\",\"RNA-seq\")","v":"RNA-seq"}]
["Experiment Description"]
["Experimental Design","growth_condition_design"]
["Experimental Design Term Source REF",{"$f":"IF(B8=\"\",\"\",\"MGED Ontology\")","v":"MGED Ontology"}]
["FungiNet Project","C3"]
[]
["# 'Experimental Factors' used to describe the variables investigated by your experiment"]
["Experimental Factor Name","pH","Medium","Oxygen_Stress"]
["Experimental Factor Type","pH","media","compound"]
["Experimental Factor Term Source REF",{"$f":"IF(B14=\"\",\"\",\"MGED Ontology\")","v":"MGED Ontology"},{"$f":"IF(C14=\"\",\"\",\"MGED Ontology\")","v":"MGED Ontology"},{"$f":"IF(D14=\"\",\"\",\"MGED Ontology\")","v":"MGED Ontology"},{"$f":"IF(E14=\"\",\"\",\"MGED Ontology\")","v":""},{"$f":"IF(F14=\"\",\"\",\"MGED Ontology\")","v":""},{"$f":"IF(#REF!=\"\",\"\",\"MGED Ontology\")","v":{"$error":"#REF!"}},{"$f":"IF(#REF!=\"\",\"\",\"MGED Ontology\")","v":{"$error":"#REF!"}}]
[]
["# Quality control information"]
["Quality Control Type"]
["Quality Control Term Source REF",{"$f":"IF(B18=\"\",\"\",\"MGED Ontology\")","v":""},{"$f":"IF(C18=\"\",\"\",\"MGED Ontology\")","v":""},{"$f":"IF(#REF!=\"\",\"\",\"MGED Ontology\")","v":{"$error":"#REF!"}},{"$f":"IF(#REF!=\"\",\"\",\"MGED Ontology\")","v":{"$error":"#REF!"}},{"$f":"IF(#REF!=\"\",\"\",\"MGED Ontology\")","v":{"$error":"#REF!"}},{"$f":"IF(#REF!=\"\",\"\",\"MGED Ontology\")","v":{"$error":"#REF!"}},{"$f":"IF(#REF!=\"\",\"\",\"MGED Ontology\")","v":{"$error":"#REF!"}}]
[]
["# Data release information"]
["Public Release Date","2015-01-27"]
["Database","GEO"]
["Accession Number","GSE61606"]
[]
["# Personal information about the data submitter(s) and investigator(s)"]
["Person Last Name","Duggan","Linde"]
["Person First Name","Seana","Jörg"]
["Person Mid Initials"]
["Person Email","Seana.Duggan@hki-jena.de","Jörg.Linde@hki-jena.de"]
["Person Phone"]
["Person Address"]
["Person Affiliation - Institution","Friedrich Schiller University Jena","Hans-Knöll-Institute Jena"]
["Person Affiliation - Department","Centre for Innovation Competence (ZIK) Septomics;Research Group Fungal Septomics","Systems Biology / Bioinformatics"]
["Person Roles","investigator","investigator; submitter"]
[]
["Cooperation partners within FungiNet - Institution"]
["Cooperation partners within FungiNet - Department"]
["Cooperation partners within SysMoDB"]
["Other cooperation partners"]
[]
["# Publications based on the data described in this file"]
["PubMed ID",25586221]
["Publication DOI or Journal/Book Title","10.1093/nar/gku1357"]
["Publication Author List","Jörg Linde;Seána Duggan;Michael Weber;Fabian Horn;Patricia Sieber;Daniela Hellwig;Konstantin Riege;Manja Marz;Ronny Martin;Reinhard Guthke; Oliver Kurzai"]
["Publication Title","Defining the transcriptomic landscape of Candida glabrata by RNA-Seq"]
["Publication Status","published"]
[]
["# Protocols (Standard Operation Procedures, SOPs)  - new protocols may only be added by the infrastructure team"]
["#","Extraction Protocols","Sequencing Protocols","Data Processing Protocols",null,null,null,null,null,"Storage Protocols"]
["Protocol Name","RNA EXTRACTION","SEQUENCING","QUALITY CONTROL OF RAW DATA","QUALITY TRIMMING OF RAW DATA","MAPPING","COUNTING","DIFFERENTIAL EXPRESSION FILTERING","ANNOTATION","STORAGE","NO STORAGE"]
["Protocol URI","rna_extraction","sequencing","qc_raw","qt_raw","mapping","counting","filtering","annotation","storage","no_storage"]
["Protocol Type","nucleic_acid_extraction","unknown_protocol_type","unknown_protocol_type","unknown_protocol_type","unknown_protocol_type","unknown_protocol_type","unknown_protocol_type","unknown_protocol_type","store","store"]
["Protocol Term Source REF","MGED Ontology","MGED Ontology","MGED Ontology",null,null,null,null,null,"MGED Ontology","MGED Ontology"]
["Protocol Description","details of RNA extraction from the biological sample","details of the sequencing process","first step of data processing","second step of data processing","third step of data processing","fourth step of data processing","details of filtering for differentially regulated genes","genome, functional and structural annotation of all genes in the dataset","storage of data ","no storage of data"]
["Protocol Parameters","260/280;230/280;RIN/RNA integrity number;Concentration;Volume;Extraction kit","Performer;Technology Type;Read Length;Library Source; Library Strategy;Library Selection; Library Layout",null,null,null,null,null,"Source, Version and Date of Annotation"]
["Protocol Hardware",null,"Illumina HiSeq 2000"]
["Protocol Software",null,null,"FastQC","btrim","tophat2","htseq-count","DESeq"]
[]
["# Controlled vocabulary sources - new sources may only be added by the data management team"]
["Term Source Name","MGED Ontology"]
["Term Source File","http://mged.sourceforge.net/ontologies/MGEDontology.php"]
["Term Source Version","1.3.1.1"]
[]
["# Filename of the 'SDRF' part belonging to this 'IDF' part"]
["SDRF File",{"$f":"MID(CELL(\"Dateiname\"),SEARCH(\"[\",CELL(\"Dateiname\"))+1,SEARCH(\"]\",CELL(\"Dateiname\"))-SEARCH(\"[\",CELL(\"Dateiname\"))-1)","v":"FungiNet_template_RNA-seq_V2.2.xlsm"}]
[]
["# Default values for filling in data automatically in the SDRF sheet (Macros must be activated)"]
[]
["# Default Biobank Material Type","whole_organism"]
["# Default Organism","Candida glabrata"]
["# Default Strain or Line","CBS138 (ATCC 2001)"]
["# Default Organism Part","all"]
["# Default Organism Status","fresh"]
["# Default Number of fungal organisms"]
["# Default Unit for number of fungal organisms"]
["# Default Sex","not applicable"]
["# Default Age",0]
["# Default Age Time Unit","hour(s)"]
["# Default Sampling Time Point"]
["# Default Sampling Time Point Unit"]
["# Default Temperature in °C",37]
["# Default Temperature Unit","degrees_C"]
["# Default pH"]
["# Default Atmosphere","air"]
["# Default Compound","none"]
["# Default Medium","M199"]
["# Default Nutrient","none"]
["# Default Biobank Storage Protocol","NO STORAGE"]
["# Default Biobank Storage Date"]
["# Default Biobank Storage Location","no storage"]
["# Default RNA Extraction Protocol","RNA EXTRACTION"]
[]
["# Default RNA Concentration"]
["# Default RNA Concentration Unit"]
["# Default RNA Volume"]
["# Default RNA Volume Unit"]
["# Default RNA Extraction Kit","RNA extraction kit"]
["# Default RNA Material Type",{"$f":"IF($B$92=\"\",\"\",\"total_RNA\")","v":"total_RNA"}]
["# Default RNA Extraction Date"]
["# Default RNA Storage Protocol","STORAGE"]
["# Default RNA Storage Date"]
["# Default RNA Storage Location","stored at ZIK septomics"]
["# Default Sequencing Protocol","SEQUENCING"]
[]
["# Default Sequencing Performer","GATC Biotech"]
["# Default Sequencing Technology Type","Sequencing by synthesis (Illumina)"]
["# Default Sequencing Read Length",50]
["# Default Sequencing Instrument",{"$f":"IF(C57=\"\",\"\",C57)","v":"Illumina HiSeq 2000"}]
["# Default Sequencing Library Source","genomic"]
["# Default Sequencing Library Strategy"]
["# Default Sequencing Library Selection","random"]
["# Default Sequencing Library Layout","single"]
["# Default Sequencing Date"]
["# Default Sequencing Storage Protocol","STORAGE"]
["# Default Sequencing Storage Date"]
["# Default Sequencing Storage Location - Server","stored at HKI Jena: /sbiarchiv"]
["# Default Sequencing Storage Location - Folder","~/jlinde/Cglabrata/rnaseq_2013_03"]
[]
["# Default Data Processing Protocol",{"$f":"IF(D58=\"\",\"\",D51)","v":"QUALITY CONTROL OF RAW DATA"}]
["# Default Data Processing Software",{"$f":"IF(D58=\"\",\"\",D58)","v":"FastQC"}]
["# Default Data Processing Protocol Parameters and Values"]
["# Default Data Processing Protocol",{"$f":"IF(E58=\"\",\"\",E51)","v":"QUALITY TRIMMING OF RAW DATA"}]
["# Default Data Processing Software",{"$f":"IF(E58=\"\",\"\",E58)","v":"btrim"}]
["# Default Data Processing Protocol Parameters and Values"]
["# Default Data Processing Protocol",{"$f":"IF(F58=\"\",\"\",F51)","v":"MAPPING"}]
["# Default Data Processing Software",{"$f":"IF(F58=\"\",\"\",F58)","v":"tophat2"}]
["# Default Data Processing Protocol Parameters and Values"]
["# Default Data Processing Protocol",{"$f":"IF(G58=\"\",\"\",G51)","v":"COUNTING"}]
["# Default Data Processing Software",{"$f":"IF(G58=\"\",\"\",G58)","v":"htseq-count"}]
["# Default Data Processing Protocol Parameters and Values"]
["# Default Data Processing Protocol",{"$f":"IF(H58=\"\",\"\",H51)","v":"DIFFERENTIAL EXPRESSION FILTERING"}]
["# Default Data Processing Software",{"$f":"IF(H58=\"\",\"\",H58)","v":"DESeq"}]
["# Default Data Processing Protocol Parameters and Values"]
[]
["# Default Data Processing Protocol","ANNOTATION"]
["# Default Genome Annotation Source","CGD"]
["# Default Genome Annotation Version","s02-m04-r01"]
["# Default Genome Annotation Date","2012-12-05"]
["# Default Genome Annotation Data File","C_glabrata_CBS138_current_chromosomal_feature.tab "]
["# Default Structural Annotation Source","CGD"]
["# Default Structural Annotation Version","s02-m05-r03"]
["# Default Structural Annotation Date"]
["# Default Structural Annotation Data File","http://www.candidagenome.org/download/gff/C_glabrata_CBS138/archive/C_glabrata_CBS138_version_s02-m05-r03_features.gff"]
["# Default Functional Annotation Source","CGD"]
["# Default Functional Annotation Version"]
["# Default Functional Annotation Date"]
["# Default Functional Annotation Data File"]
["# Default Data Processing Storage Protocol","STORAGE"]
["# Default Data Processing Storage Date"]
["# Default Data Processing Storage Location","stored at HKI Jena: /sbiarchiv"]
["# Default Data Processing Storage Location - Folder"]

{"sheet":"SDRF_example","index":3,"n_rows":25,"n_cols":100,"rows_kept":25,"cut":false,"hidden":false,"merged":[[4,92,4,96],[0,0,0,2],[4,0,4,22],[4,23,4,37],[4,38,4,53],[4,54,4,91]]}
["# Template submission sheet for FungiNet RNA-Seq experiments - Example"]
[]
[]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"IF(IDF_example!$B$14=\"age\",IF($J4=\"\",\"\",$J4),IF(IDF_example!$B$14=\"atmosphere\",IF($Q4=\"\",\"\",$Q4),IF(IDF_example!$B$14=\"organism\",IF($C4=\"\",\"\",$C4),IF(IDF_example!$B$14=\"organism_part\",IF($E4=\"\",\"\",$E4),IF(IDF_example!$B$14=\"sampling_time_point\",IF($L4=\"\",\"\",$L4),IF(IDF_example!$B$14=\"temperature\",IF($N4=\"\",\"\",$N4),IF(IDF_example!$B$14=\"pH\",IF($P4=\"\",\"\",$P4),IF(IDF_example!$B$14=\"compound\",IF($R4=\"\",\"\",$R4),IF(IDF_example!$B$14=\"media\",IF($S4=\"\",\"\",$S4),IF(IDF_example!$B$14=\"nutrients\",IF($T4=\"\",\"\",$T4),IF(IDF_example!$B$14=\"strain_or_line\",IF($D4=\"\",\"\",$D4),\"\")))))))))))","v":""},{"$f":"IF(IDF_example!$C$14=\"age\",IF($J4=\"\",\"\",$J4),IF(IDF_example!$C$14=\"atmosphere\",IF($Q4=\"\",\"\",$Q4),IF(IDF_example!$C$14=\"organism\",IF($C4=\"\",\"\",$C4),IF(IDF_example!$C$14=\"organism_part\",IF($E4=\"\",\"\",$E4),IF(IDF_example!$C$14=\"sampling_time_point\",IF($L4=\"\",\"\",$L4),IF(IDF_example!$C$14=\"temperature\",IF($N4=\"\",\"\",$N4),IF(IDF_example!$C$14=\"pH\",IF($P4=\"\",\"\",$P4),IF(IDF_example!$C$14=\"compound\",IF($R4=\"\",\"\",$R4),IF(IDF_example!$C$14=\"media\",IF($S4=\"\",\"\",$S4),IF(IDF_example!$C$14=\"nutrients\",IF($T4=\"\",\"\",$T4),IF(IDF_example!$C$14=\"strain_or_line\",IF($D4=\"\",\"\",$D4),\"\")))))))))))","v":""},null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"IF(IDF_example!$D$14=\"age\",IF($J4=\"\",\"\",$J4),IF(IDF_example!$D$14=\"atmosphere\",IF($Q4=\"\",\"\",$Q4),IF(IDF_example!$D$14=\"organism\",IF($C4=\"\",\"\",$C4),IF(IDF_example!$D$14=\"organism_part\",IF($E4=\"\",\"\",$E4),IF(IDF_example!$D$14=\"sampling_time_point\",IF($L4=\"\",\"\",$L4),IF(IDF_example!$D$14=\"temperature\",IF($N4=\"\",\"\",$N4),IF(IDF_example!$D$14=\"pH\",IF($P4=\"\",\"\",$P4),IF(IDF_example!$D$14=\"compound\",IF($R4=\"\",\"\",$R4),IF(IDF_example!$D$14=\"media\",IF($S4=\"\",\"\",$S4),IF(IDF_example!$D$14=\"nutrients\",IF($T4=\"\",\"\",$T4),IF(IDF_example!$D$14=\"strain_or_line\",IF($D4=\"\",\"\",$D4),\"\")))))))))))","v":""},{"$f":"IF(IDF_example!$E$14=\"age\",IF($J4=\"\",\"\",$J4),IF(IDF_example!$E$14=\"atmosphere\",IF($Q4=\"\",\"\",$Q4),IF(IDF_example!$E$14=\"organism\",IF($C4=\"\",\"\",$C4),IF(IDF_example!$E$14=\"organism_part\",IF($E4=\"\",\"\",$E4),IF(IDF_example!$E$14=\"sampling_time_point\",IF($L4=\"\",\"\",$L4),IF(IDF_example!$E$14=\"temperature\",IF($N4=\"\",\"\",$N4),IF(IDF_example!$E$14=\"pH\",IF($P4=\"\",\"\",$P4),IF(IDF_example!$E$14=\"compound\",IF($R4=\"\",\"\",$R4),IF(IDF_example!$E$14=\"media\",IF($S4=\"\",\"\",$S4),IF(IDF_example!$E$14=\"nutrients\",IF($T4=\"\",\"\",$T4),IF(IDF_example!$E$14=\"strain_or_line\",IF($D4=\"\",\"\",$D4),\"\")))))))))))","v":""},{"$f":"IF(IDF_example!$F$14=\"age\",IF($J4=\"\",\"\",$J4),IF(IDF_example!$F$14=\"atmosphere\",IF($Q4=\"\",\"\",$Q4),IF(IDF_example!$F$14=\"organism\",IF($C4=\"\",\"\",$C4),IF(IDF_example!$F$14=\"organism_part\",IF($E4=\"\",\"\",$E4),IF(IDF_example!$F$14=\"sampling_time_point\",IF($L4=\"\",\"\",$L4),IF(IDF_example!$F$14=\"temperature\",IF($N4=\"\",\"\",$N4),IF(IDF_example!$F$14=\"pH\",IF($P4=\"\",\"\",$P4),IF(IDF_example!$F$14=\"compound\",IF($R4=\"\",\"\",$R4),IF(IDF_example!$F$14=\"media\",IF($S4=\"\",\"\",$S4),IF(IDF_example!$F$14=\"nutrients\",IF($T4=\"\",\"\",$T4),IF(IDF_example!$F$14=\"strain_or_line\",IF($D4=\"\",\"\",$D4),\"\")))))))))))","v":""},null,{"$f":"IF($A4=\"\",\"\",\"MGED Ontology\")","v":""}]
["# Source",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"RNA Extraction",null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Sequencing",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Data Processing",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Experimental Factor Values",null,null,null,null,"Term Source","Fold Change Assignment"]
["# Specimen","Material Type","Organism","Strain or Line","Organism Part","OrganismStatus","Number of fungal organisms","Unit for number of fungi","Sex (only for mice)","Age","Age Time Unit","Sampling Time Point","Sampling Time Point Unit","Temperature in °C","Temperature Unit","pH","Atmosphere","Compound","Media","Nutrients","Storage Protocol","Storage Date","Storage Location","Extraction Protocol","Extract Name","260/280","230/280","RIN/ RNA integrity number","Concentration","Unit","Volume","Unit","Extraction Kit","Material Type","Extraction Date","Storage Protocol","Storage Date","Storage Location","Sequencing Protocol","Assay Name","Sequencing Performer","Technology Type","Read Length","Sequencing Instrument","Library Source","Library Strategy","Library Selection","Library Layout","Sequencing Date","Storage Protocol","Storage Date","Storage Location - Server","Storage Location - Folder","Data File","Data Processing Protocol","Data Processing Software","Parameters And Values","Description","Data Processing Protocol","Data Processing Software","Parameters And Values","Description","Data Processing Protocol","Data Processing Software","Parameters And Values","Description","Data Processing Protocol","Data Processing Software","Parameters And Values","Description","Data Processing Protocol","Data Processing Software","Parameters And Values","Description","Data Processing Protocol","Genome Annotation Source","Genome Annotation Version","Genome Annotation Date","Genome Annotation Data File","Structural Annotation Source","Structural Annotation Version","Structural Annotation Date","Structural Annotation Data File","Functional Annotation Source","Functional Annotation Version","Functional Annotation Date","Functional Annotation Data File","Storage Protocol","Storage Date","Storage Location - Server","Storage Location - Folder","Derived Data File",{"$f":"IF(IDF_example!B$13=\"\",\"\",IDF_example!$B13)","v":"pH"},{"$f":"IF(IDF_example!C$13=\"\",\"\",IDF_example!C$13)","v":"Medium"},{"$f":"IF(IDF_example!D$13=\"\",\"\",IDF_example!D$13)","v":"Oxygen_Stress"},{"$f":"IF(IDF_example!E$13=\"\",\"\",IDF_example!E$13)","v":""},{"$f":"IF(IDF_example!F$13=\"\",\"\",IDF_example!F$13)","v":""},"Term Source","pH4_VS_pH8","GSNO_VS_none"]
["wt_pH4_4","whole_organism","Candida glabrata","CBS138 (ATCC 2001)","all","fresh",null,null,"not applicable",0,"hour(s)",null,null,37,"degrees_C",4,"air","none","M199","none","NO STORAGE",null,"no storage","RNA EXTRACTION","wt_pH4_4_e",null,null,null,100,"μg/μl",50,"μl","RNA extraction kit",{"$f":"IF($Y7=\"\",\"\",\"total_RNA\")","v":"total_RNA"},"2012-12-05","STORAGE","2012-12-05","stored at ZIK septomics","SEQUENCING","wt_pHa_4_s","GATC Biotech","Sequencing by synthesis (Illumina)",50,"Illumina HiSeq 2000","genomic","single end; unspecific; no poly-A filter","random","single","2012-12-05","STORAGE","2012-12-05","stored at ZIK septomics",null,"lib20424_1401_5_1.fastq",{"$f":"IF(IDF_example!$D$58=\"\",\"\",IF(A7=\"\",\"\",IDF_example!$D$51))","v":"QUALITY CONTROL OF RAW DATA"},{"$f":"IF(IDF_example!$D$58=\"\",\"\",IF(A7=\"\",\"\",IDF_example!$D$58))","v":"FastQC"},"",null,{"$f":"IF(IDF_example!$E$58=\"\",\"\",IF($A7=\"\",\"\",IDF_example!$E$51))","v":"QUALITY TRIMMING OF RAW DATA"},{"$f":"IF(IDF_example!$E$58=\"\",\"\",IF($A7=\"\",\"\",IDF_example!$E$58))","v":"btrim"},"-w 15 -a 20",null,{"$f":"IF(IDF_example!$F$58=\"\",\"\",IF($A7=\"\",\"\",IDF_example!$F$51))","v":"MAPPING"},{"$f":"IF(IDF_example!$F$58=\"\",\"\",IF($A7=\"\",\"\",IDF_example!$F$58))","v":"tophat2"},"GFF (-G option) --no-mixed --no-discordant --b2-very-sensitive --max-intron-length 5000 -g 1 ",null,{"$f":"IF(IDF_example!$G$58=\"\",\"\",IF($A7=\"\",\"\",IDF_example!$G$51))","v":"COUNTING"},{"$f":"IF(IDF_example!$G$58=\"\",\"\",IF($A7=\"\",\"\",IDF_example!$G$58))","v":"htseq-count"},"--mode union --stranded no --type reverse",null,{"$f":"IF(IDF_example!$H$58=\"\",\"\",IF($A7=\"\",\"\",IDF_example!$H$51))","v":"DIFFERENTIAL EXPRESSION FILTERING"},{"$f":"IF(IDF_example!$H$58=\"\",\"\",IF($A7=\"\",\"\",IDF_example!$H$58))","v":"DESeq"},"","","ANNOTATION","CGD","s02-m04-r01","2012-12-05","C_glabrata_CBS138_current_chromosomal_feature.tab ",null,null,null,null,null,null,null,null,"STORAGE","2012-12-05","stored at HKI Jena: /sbiarchiv",null,null,{"$f":"IF(IDF_example!$B$14=\"age\",IF($J7=\"\",\"\",$J7),IF(IDF_example!$B$14=\"atmosphere\",IF($Q7=\"\",\"\",$Q7),IF(IDF_example!$B$14=\"organism\",IF($C7=\"\",\"\",$C7),IF(IDF_example!$B$14=\"organism_part\",IF($E7=\"\",\"\",$E7),IF(IDF_example!$B$14=\"sampling_time_point\",IF($L7=\"\",\"\",$L7),IF(IDF_example!$B$14=\"temperature\",IF($N7=\"\",\"\",$N7),IF(IDF_example!$B$14=\"pH\",IF($P7=\"\",\"\",$P7),IF(IDF_example!$B$14=\"compound\",IF($R7=\"\",\"\",$R7),IF(IDF_example!$B$14=\"media\",IF($S7=\"\",\"\",$S7),IF(IDF_example!$B$14=\"nutrients\",IF($T7=\"\",\"\",$T7),IF(IDF_example!$B$14=\"strain_or_line\",IF($D7=\"\",\"\",$D7),\"\")))))))))))","v":4},{"$f":"IF(IDF_example!$C$14=\"age\",IF($J7=\"\",\"\",$J7),IF(IDF_example!$C$14=\"atmosphere\",IF($Q7=\"\",\"\",$Q7),IF(IDF_example!$C$14=\"organism\",IF($C7=\"\",\"\",$C7),IF(IDF_example!$C$14=\"organism_part\",IF($E7=\"\",\"\",$E7),IF(IDF_example!$C$14=\"sampling_time_point\",IF($L7=\"\",\"\",$L7),IF(IDF_example!$C$14=\"temperature\",IF($N7=\"\",\"\",$N7),IF(IDF_example!$C$14=\"pH\",IF($P7=\"\",\"\",$P7),IF(IDF_example!$C$14=\"compound\",IF($R7=\"\",\"\",$R7),IF(IDF_example!$C$14=\"media\",IF($S7=\"\",\"\",$S7),IF(IDF_example!$C$14=\"nutrients\",IF($T7=\"\",\"\",$T7),IF(IDF_example!$C$14=\"strain_or_line\",IF($D7=\"\",\"\",$D7),\"\")))))))))))","v":"M199"},{"$f":"IF(IDF_example!$D$14=\"age\",IF($J7=\"\",\"\",$J7),IF(IDF_example!$D$14=\"atmosphere\",IF($Q7=\"\",\"\",$Q7),IF(IDF_example!$D$14=\"organism\",IF($C7=\"\",\"\",$C7),IF(IDF_example!$D$14=\"organism_part\",IF($E7=\"\",\"\",$E7),IF(IDF_example!$D$14=\"sampling_time_point\",IF($L7=\"\",\"\",$L7),IF(IDF_example!$D$14=\"temperature\",IF($N7=\"\",\"\",$N7),IF(IDF_example!$D$14=\"pH\",IF($P7=\"\",\"\",$P7),IF(IDF_example!$D$14=\"compound\",IF($R7=\"\",\"\",$R7),IF(IDF_example!$D$14=\"media\",IF($S7=\"\",\"\",$S7),IF(IDF_example!$D$14=\"nutrients\",IF($T7=\"\",\"\",$T7),IF(IDF_example!$D$14=\"strain_or_line\",IF($D7=\"\",\"\",$D7),\"\")))))))))))","v":"none"},{"$f":"IF(IDF_example!$E$14=\"age\",IF($J7=\"\",\"\",$J7),IF(IDF_example!$E$14=\"atmosphere\",IF($Q7=\"\",\"\",$Q7),IF(IDF_example!$E$14=\"organism\",IF($C7=\"\",\"\",$C7),IF(IDF_example!$E$14=\"organism_part\",IF($E7=\"\",\"\",$E7),IF(IDF_example!$E$14=\"sampling_time_point\",IF($L7=\"\",\"\",$L7),IF(IDF_example!$E$14=\"temperature\",IF($N7=\"\",\"\",$N7),IF(IDF_example!$E$14=\"pH\",IF($P7=\"\",\"\",$P7),IF(IDF_example!$E$14=\"compound\",IF($R7=\"\",\"\",$R7),IF(IDF_example!$E$14=\"media\",IF($S7=\"\",\"\",$S7),IF(IDF_example!$E$14=\"nutrients\",IF($T7=\"\",\"\",$T7),IF(IDF_example!$E$14=\"strain_or_line\",IF($D7=\"\",\"\",$D7),\"\")))))))))))","v":""},{"$f":"IF(IDF_example!$F$14=\"age\",IF($J7=\"\",\"\",$J7),IF(IDF_example!$F$14=\"atmosphere\",IF($Q7=\"\",\"\",$Q7),IF(IDF_example!$F$14=\"organism\",IF($C7=\"\",\"\",$C7),IF(IDF_example!$F$14=\"organism_part\",IF($E7=\"\",\"\",$E7),IF(IDF_example!$F$14=\"sampling_time_point\",IF($L7=\"\",\"\",$L7),IF(IDF_example!$F$14=\"temperature\",IF($N7=\"\",\"\",$N7),IF(IDF_example!$F$14=\"pH\",IF($P7=\"\",\"\",$P7),IF(IDF_example!$F$14=\"compound\",IF($R7=\"\",\"\",$R7),IF(IDF_example!$F$14=\"media\",IF($S7=\"\",\"\",$S7),IF(IDF_example!$F$14=\"nutrients\",IF($T7=\"\",\"\",$T7),IF(IDF_example!$F$14=\"strain_or_line\",IF($D7=\"\",\"\",$D7),\"\")))))))))))","v":""},{"$f":"IF($A7=\"\",\"\",\"MGED Ontology\")","v":"MGED Ontology"},"control","none"]
["wt_pH8_4","whole_organism","Candida glabrata","CBS138 (ATCC 2001)","all","fresh",null,null,"not applicable",0,"hour(s)",null,null,37,"degrees_C",8,"air","none","M199","none","NO STORAGE",null,"no storage","RNA EXTRACTION","wt_pH8_4_e",null,null,null,100,"μg/μl",50,"μl","RNA extraction kit","total_RNA","2012-12-05","STORAGE","2012-12-05","stored at ZIK septomics","SEQUENCING","wt_pHb_4_s","GATC Biotech","Sequencing by synthesis (Illumina)",50,"Illumina HiSeq 2000","genomic","single end; unspecific; no poly-A filter","random","single","2012-12-05","STORAGE","2012-12-05","stored at ZIK septomics",null,"lib20425_1401_5_1.fastq",{"$f":"IF(IDF_example!$D$58=\"\",\"\",IF(A8=\"\",\"\",IDF_example!$D$51))","v":"QUALITY CONTROL OF RAW DATA"},{"$f":"IF(IDF_example!$D$58=\"\",\"\",IF(A8=\"\",\"\",IDF_example!$D$58))","v":"FastQC"},"",null,{"$f":"IF(IDF_example!$E$58=\"\",\"\",IF($A8=\"\",\"\",IDF_example!$E$51))","v":"QUALITY TRIMMING OF RAW 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