{"text_format":"3","workbook":"xlsx","n_sheets":4,"sheets":["infos échantillons","Ressource","Version","Feuil1"],"not_rendered":{"defined_names":10,"comments":1},"read":"whole","date_system":"1900"}

{"sheet":"infos échantillons","index":0,"n_rows":1947,"n_cols":16,"rows_kept":1947,"merged":[[0,0,0,3],[0,4,0,9],[2,1,2,2],[2,3,2,4],[2,5,2,6],[2,7,2,8],[11,1,11,3],[11,5,12,9],[12,1,12,3],[13,1,13,2],[14,1,14,2],[15,1,15,2],[16,1,16,2],[16,5,16,9],[17,1,17,2],[17,5,17,9],[18,1,18,2],[19,1,19,2],[20,1,20,2],[21,1,21,2],[22,1,22,2],[23,1,23,2],[25,0,25,15]]}
["Fiche échantillon pour le projet  : "]
[]
[null," Pré-requis ADN TruSeq Nano \n(avec amplification PCR)",null,"Pré-requis ADN PCRfree\n (sans amplification PCR)",null,"Pré-requis ADN Mate-Pair",null," Pré-requis ADN EMseq\n"]
[null,"Qté min. de matrice :","300 ng","Qté min. de matrice :","4µg","Qté min. de matrice :","5 µg","Qté min. de matrice :","300 ng"]
[null,"concentration min. :","5 ng/µl","concentration min. :","57ng/µl","concentration min. :","32 ng/µl","concentration min. :","5 ng/µl"]
[null,"Pureté 260/280 :","1,8","Pureté 260/280 :","1,8","Pureté 260/280 :","1,8","Pureté 260/280 :","1,8"]
[null,"Pureté 260/230 :","1,8","Pureté 260/230 :","1,8","Pureté 260/230 :","1,8","Pureté 260/230 :","1,8"]
[]
[]
[null,"Consultez le document Prérequis pour plus d'information"]
[]
[null,"A renseigner par l'équipe de recherche",{"$nulls":3},"Merci de ne pas modifier ni l'emplacement des colonnes ni leurs titres"]
[]
[null,"Nature de la matrice",null,null,{"$f":"IFERROR(INDEX(Ressource!A3:B11,MATCH(D14,Ressource!A3:A11,0),2),\"\")","v":""}]
[null,"Type de librairie",null,null,{"$f":"IFERROR(INDEX(Ressource!E3:F38,MATCH(D15,Ressource!E3:E38,0),2),\"A remplir si Ready-To-Load\")","v":"A remplir si Ready-To-Load"},"a si vos échantillons ne valident pas les pré-requis, contacter la plateforme"]
[null,"Sélection de librairie",null,null,{"$f":"IFERROR(INDEX(Ressource!C3:D33,MATCH(D16,Ressource!C3:C33,0),2),\"A remplir si Ready-To-Load\")","v":"A remplir si Ready-To-Load"}]
[null,"Espèce (nom scientifique)",{"$nulls":3},"* Si le support de vos échantillons (tube, plaque) a un code-barres, merci de le spécifier dans la colonne Code-barres"]
[null,"Méthode d'extraction",{"$nulls":3},"* Choisir des noms d'échantillons courts sans caractères spéciaux (espaces, virgules, points, underscores …) sauf tiret toléré"]
[null,"Elution",{"$nulls":3},"* Vérifier que le nom sur le tube correspond au nom inscrit dans le fichier"]
[null,"Nombre d'échantillons",{"$nulls":3},"* Afin de réaliser les analyses qualité de vos données, merci de nous fournir le lien web vers le génome de référence et sa version"]
[null,"Nombre de lanes"]
[null,"Multiplexage",null,"n-plex / non"]
[]
[null,"Identifiant/lien Génome de référence ( NCBI/Ensembl…)"]
[]
["Informations sur les échantillons à renseigner par l'équipe de recherche"]
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{"sheet":"Ressource","index":1,"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).","RANDOM"," No Selection or Random selection","WGS"," Whole Genome Sequencing - random sequencing of the whole genome (see pubmed 10731132 for details)"]
["GENOMIC SINGLE CELL","No description","PCR"," target enrichment via PCR","WGA"," Whole Genome Amplification followed by random sequencing. (see pubmed 1631067,8962113 for details)"]
["TRANSCRIPTOMIC"," Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries).","RANDOM PCR"," Source material was selected by randomly generated primers.","WXS"," Random sequencing of exonic regions selected from the genome. (see pubmed 20111037 for details)"]
["TRANSCRIPTOMIC SINGLE CELL","No description","RT-PCR"," target enrichment via","RNA-Seq"," Random sequencing of whole transcriptome, also known as Whole Transcriptome Shotgun Sequencing, or WTSS). (see pubmed 18611170 for details)"]
["METAGENOMIC"," Mixed material from metagenome.","HMPR"," Hypo-methylated partial restriction digest","ssRNA-seq"," Strand-specific RNA sequencing."]
["METATRANSCRIPTOMIC"," Transcription products from community targets","MF"," Methyl Filtrated","miRNA-Seq"," Micro RNA sequencing strategy designed to capture post-transcriptional RNA elements and include non-coding functional elements. (see pubmed 21787409 for details)"]
["SYNTHETIC"," Synthetic DNA.","repeat fractionation"," Selection for less repetitive (and more gene rich) sequence through Cot filtration (CF) or other fractionation techniques based on DNA kinetics.","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)."]
["VIRAL RNA"," Viral RNA.","size fractionation"," Physical selection of size appropriate targets.","FL-cDNA"," Full-length sequencing of cDNA templates"]
["OTHER"," Other, unspecified, or unknown library source material.","MSLL"," Methylation Spanning Linking Library","EST"," Single pass sequencing of cDNA templates"]
[null,null,"cDNA"," PolyA selection or enrichment for messenger RNA (mRNA); synonymize with PolyA","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,"cDNA_randomPriming","No description","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."]
[null,null,"cDNA_oligo_dT","No description","WCS"," Random sequencing of a whole chromosome or other replicon isolated from a genome."]
[null,null,"PolyA"," PolyA selection or enrichment for messenger RNA (mRNA); should replace cDNA enumeration.","RAD-Seq","No description"]
[null,null,"Oligo-dT"," enrichment of messenger RNA (mRNA) by hybridization to Oligo-dT.","CLONE"," Genomic clone based (hierarchical) sequencing."]
[null,null,"Inverse rRNA"," depletion of ribosomal RNA by oligo hybridization.","POOLCLONE"," Shotgun of pooled clones (usually BACs and Fosmids)."]
[null,null,"Inverse rRNA selection"," depletion of ribosomal RNA by inverse oligo hybridization.","AMPLICON"," Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA."]
[null,null,"ChIP"," Chromatin immunoprecipitation","CLONEEND"," Clone end (5’, 3’, or both) sequencing."]
[null,null,"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.","FINISHING"," Sequencing intended to finish (close) gaps in existing coverage."]
[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.","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."]
[null,null,"DNase"," DNase I endonuclease digestion and size selection reveals regions of chromatin where the DNA is highly sensitive to DNase I.","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,"Hybrid Selection"," Selection by hybridization in array or solution.","DNase-Hypersensitivity"," Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI."]
[null,null,"Reduced Representation"," Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling.","Bisulfite-Seq"," MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status."]
[null,null,"Restriction Digest"," DNA fractionation using restriction enzymes.","CTS"," Concatenated Tag Sequencing"]
[null,null,"5-methylcytidine antibody"," Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C).","MRE-Seq"," Methylation-Sensitive Restriction Enzyme Sequencing."]
[null,null,"MBD2 protein methyl-CpG binding domain"," Enrichment by methyl-CpG binding domain.","MeDIP-Seq"," Methylated DNA Immunoprecipitation Sequencing."]
[null,null,"CAGE"," Cap-analysis gene expression.","MBD-Seq"," Methyl CpG Binding Domain Sequencing."]
[null,null,"RACE"," Rapid Amplification of cDNA Ends.","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,"MDA"," Multiple Displacement Amplification, a non-PCR based DNA amplification technique that amplifies a minute quantifies of DNA to levels suitable for genomic analysis.","VALIDATION","  CGHub special request:  Independent experiment to re-evaluate putative variants."]
[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).","FAIRE-seq"," Formaldehyde Assisted Isolation of Regulatory Elements. Reveals regions of open chromatin."]
[null,null,"other"," Other library enrichment, screening, or selection process.","SELEX"," Systematic Evolution of Ligands by Exponential enrichment"]
[null,null,"unspecified"," Library enrichment, screening, or selection is not specified.","RIP-Seq"," Direct sequencing of RNA immunoprecipitates (includes CLIP-Seq, HITS-CLIP and PAR-CLIP)."]
[{"$nulls":4},"ChIA-PET"," Direct sequencing of proximity-ligated chromatin immunoprecipitates."]
[{"$nulls":4},"Synthetic-Long-Read"," binning and barcoding of large DNA fragments to facilitate assembly of the fragment"]
[{"$nulls":4},"Targeted-Capture"," Enrichment of a targeted subset of loci."]
[{"$nulls":4},"Tethered Chromatin Conformation Capture"]
[{"$nulls":4},"OTHER"," Library strategy not listed."]

{"sheet":"Version","index":2,"n_rows":6,"n_cols":3,"rows_kept":6}
["Date","Quoi","Qui"]
["2023-04-12T22:42:00"]
["2023-08-07T18:03:00","ajout infos pour metadata ENA (lib, espèce)","Gérald"]
["2023-08-24T19:12:00","Uniformisation cellules genome et transcriptome","Gérald"]
["2023-08-24T19:12:00","Uniformisation cellules genome et transcriptome","Gérald"]
["2023-09-29T15:37:00","précision remplir les infos de lib si RTL","Gérald"]

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