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["Technique"]
["Machine"]
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[]
[]
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[null,null,"Library type"]
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[null,null,"Library selection"]
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[null,null,"Pool concentration (nM)"]
[null,null,"Pool volume (µL)"]
[null,null,"Pool average size (pb)"]
[null,null,"% PhiX to include"]
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[null,null,"Indexing type"]
[null,null,"Index kit name"]
[null,null,"Comment"]
[]
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["No Index"]

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[null,"2x150 Micro V2 (MiSeq)"]
[null,"2x150 Nano V2 (MiSeq)"]
[null,"2x250 Nano V2 (MiSeq)"]
[null,"2x150 V2 (MiSeq)"]
[null,"2x250 V2 (MiSeq)"]
[null,"2x75 V3 (MiSeq)"]
[null,"2x250 V3 (MiSeq)"]
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{"sheet":"Réservé à PlaGe","index":2,"n_rows":1,"n_cols":1,"rows_kept":1}
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{"sheet":"Lane","index":3,"n_rows":999,"n_cols":36,"rows_kept":999}
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["Concentration librairie en qPCR(nM)",{"$f":"IF(B19=\"pur\",B22,IF(B19=\"dilution 1\",B25,IF(B19=\"dilution 2\",B28,IF(B19=\"dilution 3\",B31,\"\"))))","v":0},{"$nulls":4},0,{"$nulls":16},0,0,0,"","","",{"$nulls":3},"","","",""]
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["Pool average size (pb)",{"$nulls":5},0,{"$nulls":16},0,0,0,"","","",{"$nulls":3},"","","",""]
["Vol. final pool (µl)",{"$f":"IFERROR(SUM(AC2:AC999),0)","v":{"v":0,"d":"0.00"}},{"$nulls":4},0,{"$nulls":16},0,0,0,"","","",{"$nulls":3},"","","",""]
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["Localisation actuelle",{"$nulls":5},0,{"$nulls":16},0,0,0,"","","",{"$nulls":3},"","","",""]
["Localisation de reference",{"$nulls":5},0,{"$nulls":16},0,0,0,"","","",{"$nulls":3},"","","",""]
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["Code-barre Pool pur",{"$nulls":5},0,{"$nulls":16},0,0,0,"","",""]
["Concentration estimée (nM)",{"$f":"IFERROR((SUM(AA2:AA41)/B13),0)","v":{"v":0,"d":"0.00"}},{"$nulls":4},0,{"$nulls":16},0,0,0,"","",""]
["Concentration dosée pure",{"$nulls":5},0,{"$nulls":16},0,0,0,"","","",{"$nulls":3},{"$f":"IF(E22<>\"\",E22,\"\")","v":""},{"$f":"IF(N22<>\"\",N22,\"\")","v":""},{"$f":"IF(Q22<>\"\",Q22,\"\")","v":""},{"$f":"IF(U22<>\"\",U22,\"\")","v":""}]
["Nom dilution 1",{"$nulls":5},0,{"$nulls":16},0,0,0,"","","",{"$nulls":3},{"$f":"IF(E23<>\"\",E23,\"\")","v":""},{"$f":"IF(N23<>\"\",N23,\"\")","v":""},{"$f":"IF(Q23<>\"\",Q23,\"\")","v":""},{"$f":"IF(U23<>\"\",U23,\"\")","v":""}]
["Code-barre dilution 1",{"$nulls":5},0,{"$nulls":16},0,0,0,"","",""]
["Concentration dilution 1",{"$nulls":5},0,{"$nulls":16},0,0,0,"","","",{"$nulls":3},{"$f":"IF(E25<>\"\",E25,\"\")","v":""},{"$f":"IF(N25<>\"\",N25,\"\")","v":""},{"$f":"IF(Q25<>\"\",Q25,\"\")","v":""},{"$f":"IF(U25<>\"\",U25,\"\")","v":""}]
["Nom dilution 2",{"$nulls":5},0,{"$nulls":16},0,0,0,"","","",{"$nulls":3},{"$f":"IF(E26<>\"\",E26,\"\")","v":""},{"$f":"IF(N26<>\"\",N26,\"\")","v":""},{"$f":"IF(Q26<>\"\",Q26,\"\")","v":""},{"$f":"IF(U26<>\"\",U26,\"\")","v":""}]
["Code-barre dilution 2",{"$nulls":5},0,{"$nulls":16},0,0,0,"","",""]
["Concentration dilution 2",{"$nulls":5},0,{"$nulls":16},0,0,0,"","","",{"$nulls":3},{"$f":"IF(E28<>\"\",E28,\"\")","v":""},{"$f":"IF(N28<>\"\",N28,\"\")","v":""},{"$f":"IF(Q28<>\"\",Q28,\"\")","v":""},{"$f":"IF(U28<>\"\",U28,\"\")","v":""}]
["Nom dilution 3",{"$nulls":5},0,{"$nulls":16},0,0,0,"","","",{"$nulls":3},{"$f":"IF(E29<>\"\",E29,\"\")","v":""},{"$f":"IF(N29<>\"\",N29,\"\")","v":""},{"$f":"IF(Q29<>\"\",Q29,\"\")","v":""},{"$f":"IF(U29<>\"\",U29,\"\")","v":""}]
["Code-barre dilution 3",{"$nulls":5},0,{"$nulls":16},0,0,0,"","",""]
["Concentration dilution 3",{"$nulls":5},0,{"$nulls":16},0,0,0,"","","",{"$nulls":3},{"$f":"IF(E31<>\"\",E31,\"\")","v":""},{"$f":"IF(N31<>\"\",N31,\"\")","v":""},{"$f":"IF(Q31<>\"\",Q31,\"\")","v":""},{"$f":"IF(U31<>\"\",U31,\"\")","v":""}]
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{"sheet":"Ressource","index":4,"n_rows":38,"n_cols":6,"rows_kept":38,"merged":[[0,0,0,1],[0,2,0,3],[0,4,0,5]]}
["Type of DNA or RNA used in the experiment",null,"Whether the source material was selected for certain properties (for\nexample methyl filtrated)",null,"The sequencing technique intended for the library."]
["library source","library source explanation","library selection","library selection explanation","Library strategy","Library strategy explanation"]
["GENOMIC"," Genomic DNA (includes PCR products from genomic DNA).","5-methylcytidine antibody"," Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C).","AMPLICON"," Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA."]
["GENOMIC SINGLE CELL","No description","CAGE"," Cap-analysis gene expression.","ATAC-seq"," Assay for Transposase-Accessible Chromatin (ATAC) strategy is used to study genome-wide chromatin accessibility. alternative method to DNase-seq that uses an engineered Tn5 transposase to cleave DNA and to integrate primer DNA sequences into the cleaved genomic DNA."]
["METAGENOMIC"," Mixed material from metagenome.","cDNA"," PolyA selection or enrichment for messenger RNA (mRNA); synonymize with PolyA","Bisulfite-Seq"," MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status."]
["METATRANSCRIPTOMIC"," Transcription products from community targets","cDNA_oligo_dT","No description","ChIA-PET"," Direct sequencing of proximity-ligated chromatin immunoprecipitates."]
["SYNTHETIC"," Synthetic DNA.","cDNA_randomPriming","No description","ChIP-Seq"," ChIP-seq, Chromatin ImmunoPrecipitation, reveals binding sites of specific proteins, typically transcription factors (TFs) using antibodies to extract DNA fragments bound to the target protein."]
["TRANSCRIPTOMIC"," Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries).","ChIP"," Chromatin immunoprecipitation","CLONE"," Genomic clone based (hierarchical) sequencing."]
["TRANSCRIPTOMIC SINGLE CELL","No description","ChIP-Seq"," Chromatin immunoPrecipitation, reveals binding sites of specific proteins, typically transcription factors (TFs) using antibodies to extract DNA fragments bound to the target protein.","CLONEEND"," Clone end (5’, 3’, or both) sequencing."]
["VIRAL RNA"," Viral RNA.","DNase"," DNase I endonuclease digestion and size selection reveals regions of chromatin where the DNA is highly sensitive to DNase I.","CTS"," Concatenated Tag Sequencing"]
["OTHER"," Other, unspecified, or unknown library source material.","HMPR"," Hypo-methylated partial restriction digest","DNase-Hypersensitivity"," Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI."]
[null,null,"Hybrid Selection"," Selection by hybridization in array or solution.","EST"," Single pass sequencing of cDNA templates"]
[null,null,"Inverse rRNA"," depletion of ribosomal RNA by oligo hybridization.","FAIRE-seq"," Formaldehyde Assisted Isolation of Regulatory Elements. Reveals regions of open chromatin."]
[null,null,"Inverse rRNA selection"," depletion of ribosomal RNA by inverse oligo hybridization.","FINISHING"," Sequencing intended to finish (close) gaps in existing coverage."]
[null,null,"MBD2 protein methyl-CpG binding domain"," Enrichment by methyl-CpG binding domain.","FL-cDNA"," Full-length sequencing of cDNA templates"]
[null,null,"MDA"," Multiple Displacement Amplification, a non-PCR based DNA amplification technique that amplifies a minute quantifies of DNA to levels suitable for genomic analysis.","Hi-C"," Chromosome Conformation Capture technique where a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing."]
[null,null,"MF"," Methyl Filtrated","MBD-Seq"," Methyl CpG Binding Domain Sequencing."]
[null,null,"MNase"," Identifies well-positioned nucleosomes. uses Micrococcal Nuclease (MNase) is an endo-exonuclease that processively digests DNA until an obstruction, such as a nucleosome, is reached.","MeDIP-Seq"," Methylated DNA Immunoprecipitation Sequencing."]
[null,null,"MSLL"," Methylation Spanning Linking Library","miRNA-Seq"," Micro RNA sequencing strategy designed to capture post-transcriptional RNA elements and include non-coding functional elements. (see pubmed 21787409 for details)"]
[null,null,"Oligo-dT"," enrichment of messenger RNA (mRNA) by hybridization to Oligo-dT.","MNase-Seq"," Identifies well-positioned nucleosomes. uses Micrococcal Nuclease (MNase) is an endo-exonuclease that processively digests DNA until an obstruction, such as a nucleosome, is reached."]
[null,null,"padlock probes capture method"," Targeted sequence capture protocol covering an arbitrary set of nonrepetitive genomics targets. An example is capture bisulfite sequencing using padlock probes (BSPP).","MRE-Seq"," Methylation-Sensitive Restriction Enzyme Sequencing."]
[null,null,"PCR"," target enrichment via PCR","ncRNA-Seq"," Capture of other non-coding RNA types, including post-translation modification types such as snRNA (small nuclear RNA) or snoRNA (small nucleolar RNA), or expression regulation types such as siRNA (small interfering RNA) or piRNA/piwi/RNA (piwi-interacting RNA)."]
[null,null,"PolyA"," PolyA selection or enrichment for messenger RNA (mRNA); should replace cDNA enumeration.","POOLCLONE"," Shotgun of pooled clones (usually BACs and Fosmids)."]
[null,null,"RACE"," Rapid Amplification of cDNA Ends.","RAD-Seq","No description"]
[null,null,"RANDOM"," No Selection or Random selection","RIP-Seq"," Direct sequencing of RNA immunoprecipitates (includes CLIP-Seq, HITS-CLIP and PAR-CLIP)."]
[null,null,"RANDOM PCR"," Source material was selected by randomly generated primers.","RNA-Seq"," Random sequencing of whole transcriptome, also known as Whole Transcriptome Shotgun Sequencing, or WTSS). (see pubmed 18611170 for details)"]
[null,null,"Reduced Representation"," Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling.","SELEX"," Systematic Evolution of Ligands by Exponential enrichment"]
[null,null,"repeat fractionation"," Selection for less repetitive (and more gene rich) sequence through Cot filtration (CF) or other fractionation techniques based on DNA kinetics.","ssRNA-seq"," Strand-specific RNA sequencing."]
[null,null,"Restriction Digest"," DNA fractionation using restriction enzymes.","Synthetic-Long-Read"," binning and barcoding of large DNA fragments to facilitate assembly of the fragment"]
[null,null,"RT-PCR"," target enrichment via","Targeted-Capture"," Enrichment of a targeted subset of loci."]
[null,null,"size fractionation"," Physical selection of size appropriate targets.","Tethered Chromatin Conformation Capture"]
[null,null,"other"," Other library enrichment, screening, or selection process.","Tn-Seq"," Quantitatively determine fitness of bacterial genes based on how many times a purposely seeded transposon gets inserted into each gene of a colony after some time."]
[null,null,"unspecified"," Library enrichment, screening, or selection is not specified.","VALIDATION","  CGHub special request:  Independent experiment to re-evaluate putative variants."]
[{"$nulls":4},"WCS"," Random sequencing of a whole chromosome or other replicon isolated from a genome."]
[{"$nulls":4},"WGA"," Whole Genome Amplification followed by random sequencing. (see pubmed 1631067,8962113 for details)"]
[{"$nulls":4},"WGS"," Whole Genome Sequencing - random sequencing of the whole genome (see pubmed 10731132 for details)"]
[{"$nulls":4},"WXS"," Random sequencing of exonic regions selected from the genome. (see pubmed 20111037 for details)"]
[{"$nulls":4},"OTHER"," Library strategy not listed."]

{"sheet":"Version","index":5,"n_rows":14,"n_cols":3,"rows_kept":14}
["date","quoi","qui"]
["2023-07-27T09:03:00","ajout infos pour metadata ENA (lib, espèce, taxo)","Gérald"]
["2023-08-29T16:34:00","ajout possibilité de créer des worklists\najout liens vers ENA\ncalcul automatique de la taille moyenne d'insert du pool","Gérald"]
["2023-09-18T09:09:00","translate to english\nupdate macro to manage english version","Rachel/Eden\nGérald"]
["2023-10-02T10:38:00","mise à jour macro de calcul de volume de la lib pour la ligne 2\najout de contraintes pour certaines colonnes attendant des volumes ","Gérald"]
["2023-10-24T11:52:00","allow up to 1536 libs\ncorrect lib name validation to not allow -- and and space or dash at the end of the name","Gérald"]
["2024-03-13T10:37:00","block if species is not set or not found\ndo not make kit name mandatory for sample names validation\nblock if sample name does not respect constraint","Gérald"]
["2024-04-10T12:06:00","display a message to check administrative task after clicking on button 4","Gérald"]
["2024-06-25T16:10:00","Warn user if different run names are set for a pool (or different lib sizes  for an amplicon run)","Gérald"]
["2024-06-25T16:10:00","Remove sequence OK which is not useful anymore","Gérald"]
["2024-06-27T12:52:00","replace \"Library diversity\" with \"%PhiX to include\"\nReplace \"Taille Insert (pb)\" with \"Pool size (pb)\" in Lane sheet","Gérald"]
["2024-07-19T08:35:00","Change %PhiX to include cell format to numeric","Gérald"]
["2024-11-08T16:08:00","Add AVITI Flowcells ","Léo"]
["2024-12-06T08:47:00","add volumes for pool and lib","Léo/Gérald"]

{"sheet":"Pool Robot","index":6,"n_rows":1,"n_cols":5,"rows_kept":1,"hidden":true}
["SourceLabwareLabel","Source Position","Volumes","Destination Labware Label","Destination Position"]