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["Fiche échantillon pour le projet  : "]
[]
[null,"Pré-requis ADN ONT et PACBIO",{"$nulls":3},"Merci de ne pas modifier ni l'emplacement des colonnes ni leurs titres"]
[null,"Qté min. de matrice (Qubit) :","10µg pour une Flowcell ONT ou une SMRTcell PACBIO en simplex\n4µg par échantillons pour un multiplex"]
[null,"concentration min-max :","30 - 500 ng/µl"]
[null,"Pureté 260/280 :","1,8-2",null,null,"a si vos échantillons ne valident pas les pré-requis, contacter la plateforme"]
[null,"Pureté 260/230 :","2-2,2"]
[null,"Taille ADN minimum :",">20kb",null,null,"* Choisir des noms d'échantillons courts sans caractères spéciaux (espaces, virgules, points, underscores …) sauf tiret toléré"]
[{"$nulls":5},"* Vérifier que le nom sur le tube correspond au nom inscrit dans le fichier"]
[]
[null,"Consultez le document Prérequis pour plus d'information"]
[]
[null,"A renseigner par l'équipe de recherche"]
[]
[null,"Nature de la matrice",null,"GENOMIC",{"$f":"IFERROR(INDEX(Ressource!A3:B11,MATCH(D15,Ressource!A3:A11,0),2),\"\")","v":" Genomic DNA (includes PCR products from genomic DNA)."}]
[null,"Type de librairie",null,null,{"$f":"IFERROR(INDEX(Ressource!E3:F38,MATCH(D16,Ressource!E3:E38,0),2),\"A remplir si Ready-To-Load\")","v":"A remplir si Ready-To-Load"}]
[null,"Sélection de librairie",null,null,{"$f":"IFERROR(INDEX(Ressource!C3:D33,MATCH(D17,Ressource!C3:C33,0),2),\"A remplir si Ready-To-Load\")","v":"A remplir si Ready-To-Load"}]
[null,"Espèce (nom scientifique)"]
[null,"Tampon d'Elution"]
[null,"Nombre d'échantillons"]
[null,"PHOTO GEL"]
[null,"Taille Ladder"]
[]
[null,"Identifiant/lien Génome de référence ( NCBI/Ensembl…)"]
[]
[]
[]
["Informations sur les échantillons à renseigner par l'équipe de recherche"]
[null,"Nom Echantillon","Espèce (nom scientifique)","Dosage NanoDrop (ng/µl)","ratio 260/280","ratio 260/230","Dosage au QuBit  ou Picogreen (ng/µl)","Volume (µl)","Quantité fournie (µg)","Méthode d'extraction","Commentaire (texture, couleur, aspect..)","Nature de la matrice","Type de librairie","Sélection de librairie"]
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["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":2,"n_rows":4,"n_cols":3,"rows_kept":4}
["Date","Quoi","Qui"]
["2023-02-27T18:26:00"]
["2023-08-10T18:03:00","ajout infos pour metadata ENA (lib, espèce)","Gérald"]
["2023-09-29T15:37:00","précision remplir les infos de lib si RTL","Gérald"]

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