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Metadata sheet per Sample
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All fields marked with * are mandatory. Enter your details in column E.
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Example values for each field is provided in column D for aid with filling the sheet.
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Make edits only in column E. Do not change the field names.
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Enter information and contact details of the lab, PI and submitter in submission information fields.ExampleYour sample details
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Submission informationPlatform*Illumina NovaSeqXIllumina NovaSeqX 10B XP flowcell PairedEnd 150Illumina NovaSeqX 10B XP flowcell PairedEnd 150
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Project ID*Unique ID associated to all the samples of this submissionSmith_m6A_seqSample 369647
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Submission date*Date when sequencing data were upload1/10/20262/18/2026
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Submission author*Person doing the submissionJane DoeChristoph Dieterich / Michael Jantsch
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Submission author email*Email from person doing the submissionjane.doe@university.educhristoph.dieterich@uni-heidelberg.de
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Laboratory head/PI*PI's last nameSmithDieterich / Jantsch
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Contact email*PI's email or other contact emailj.smith@university.educhristoph.dieterich@uni-heidelberg.de; Michael.Jantsch@meduniwien.ac.at
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Study title*Replicate numberm6A mapping in human cell linesinosine detection in RNA-seq reads
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Modification type*The specific RNA modification targeted.m6Ainosine
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Modification typeIf modification type selected is Other, mention the specific modification
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Modification detection strategy*The sequencing strategy (RNA-Seq / MeRIP-Seq / m6A-seq / eCLIP / miCLIP / RIP-Seq / DART-seq / bisulfite-RNA / ICE-Seq / RiboMethSeq / other (specify))GLORI-seqOther
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Modification detection strategyIf modification detection strategy selected in Other, mention the specific methodplain RNA sequencing
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Method specific information*Description of method for modification detection strategyUnmodified adenosine bases were converted to inosine (read as G during sequencing) leaving m6A bases intact (read as A during sequencing)
Inosine is interpreted as Guanosine during cDNA synthesis. Therefore any A to G differences between genomic DNA and RNA can be interpreted as an adenosine deamination event
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Brief description of the sample manipulation prior to library prep*Brief description of the manipulationChemical conversion of unmodified bases to inosine by glyoxal and nitrite
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Sample RNASample name*Unique sample name associated to your submissionSmith_GM12878_GLORI_m6ASample 369647
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Sample type*RNA biotypemRNAmRNA
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Sample description*Description of the sample being processed
Poly(A) RNA was selected and fragmented from the source RNA.
Total RNA, NEB rRNA depletion kit
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RIN value*RIN value of sample prior to starting library prep99.7
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Replicate information*Replicate number (of total number of replicates)Rep1 (of 3)1
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Enter information for the appropriate epitranscriptomics method used in the experiment.
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Only enter information for one sample per method. Create multiple sheets for additional methods and samples
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Epitranscriptomics method
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Enzymatic methodEnzyme nameName of the enzyme used for modification detectionAPOBEC1-YTH
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Enzyme vendor nameName of the vendor from where the enzyme was sourcedThermo Fisher Scientific
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Enzyme catalog numberCatalog number of the enzyme in vendor catalog912902
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Units per reactionNumber of units of enzyme used per reaction4U
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Digestion conditionsMention specific digestion conditions37°C for 15 minutes
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Expected conversion/cleavage siteMotif or specific cleavage/modification site of the enzymeAt C residue downstream of m6A site
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Enzyme controlsmock/no-enzyme control (yes/no)yes
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Chemical methodChemical reagentName of the chemical used for modification detectionGlyoxal and nitrite
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Reagent vendor nameName of the vendor from where the chemical was sourcedSigma-aldrich
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Reagent catalog numberCatalog number of the chemical in vendor catalog128465
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ConcentrationConcentration of chemical used for modification detection0.1M
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Reaction conditionMention specific reaction conditions for modification detectionThe RNA is incubated with glyoxal at an acidic pH, such as pH 6.0 (using a MES buffer), at an elevated temperature, such as 50 °C. Sodium nitrite is added to the reaction mixture. The reaction is typically carried out at the same temperature as the glyoxal treatment (e.g., 50 °C) for 5 minutes. 
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Quenching conditionMention specific quenching conditions for modification detectionRNA purification
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Conversion efficiency controlProvide list of spike-in or knownsite controls for measuring conversion efficiency (if any)
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RT enzyme based methodsRT enzymeName of the RT enzyme used for modification detectionTGIRT
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RT primersChoose RT primer strategy (random hexamers, oligo(dT), gene specific)random hexamers
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RT conditionsMention specific RT conditions for RT reactionSpecific buffer conditions
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RT temperatureMention temperature and duration used for RT reaction60 °C x 30mins
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Anti-m6A antibody
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AntibodyAntibody nameCommon name of the antibody
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Antibody vendorName of the vendorSynaptic Systems
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Antibody catalogCatalog number from vendor for the antibody202 003
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Antibody host isotypeHost type of the antibody usedRabbit IgG
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Amount per reactionAmount of antibody used per reaction5 µg
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Incubation conditionsDescription of incubation conditions such as buffer, temperature, time etc.4°C for 2 hours on a rotator
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Bead typeType of beads used for enrichmentProtein A/G magnetic beads
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Input fraction usedfraction (%) of input used relative to IP10%
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IgG control usedYes/no, whether Ig control usedYes
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Cross LinkingType of method used for cross-linking (if any)UV 254nm
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Assay nameName of the assay performed for the sampleMeRIP
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Assay typeType of assay performed for sampleImmunoprecipitation
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Assay protocolDescription of protocol performed for the assayAttach protocol
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Enter information related to library and library preparation method.
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LibraryLibrary name*A unique name for each librarySmith_m6A_GLORI_seqSample 369647
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Library kit*Sequencing kit, vendor and catalog no. of the library preparation kitNEBNext Ultra II Directional RNA Library PrepNEBNext 96 Unique Dual Index Primer Pairs UMI cat E787
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Library selection*How the library was selected/enriched.E7760E7878
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Library construction protocol*Description of how the library was prepared from RNAN/AN/A
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Adapter sequence*Sequence of adapter usedAMPure XP beads718:7-314-B3:CTGGACACNNNNNNNNNNNN 518:5-362-B3:TACTGTGA
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PCR cycles*Number of PCR cycles used during library preparation
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Library size range*Range of library fragment lengths300412
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Replicate group*Libraries that are replicates should have identical replicate group namesCell_line_A_rep1
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Input library*Yes/No. Whether the sample is an "Input" control or an "IP" / "Treated" library.Nono
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Library layout*single-end or paired-end.paired-endpaired end
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UMI present*Yes/NoYesyes
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UMI patternPattern of UMI used for the sample6N12N
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Library enrichment methodUMI treatment, circularization, ligation specifics, PCR, etc.PCR (12 cycles)UMI treatment
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Enter information related to the sequencing instrument and read statistics.
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SequencingInstrument model*Description of the sequencer model usedIllumina NovaSeq 6000Illumina NovaSeqX 10B XP flowcell PairedEnd 150
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Read length*Length of read generated for the sample150150
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Mean quality*Mean quality of sequencing run35>30
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Read counts*Number of reads generated for the sample50,000,000860,400,000
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Spike insAny spike-in controls added (eg., ERCC RNA spike-in mix, etc.)ERCC RNA Spike-In Mix 11% PhiX
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Enter information of the files and md5sum for the files to be uploaded.
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Two fastq files for paired end read sequencing and one fastq file for single end read sequencing is expected.
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If more files are to be uploaded, add rows below.
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FileFile name*Unique file name of the uploaded fileSmith_m6A_GLORI_seq_rep1_R1.fastq.gz23GCFKLT3_7_R19973_20260116.tar.gz
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File MD5sum*MD5sum for the uploaded filed41d8cd98f00b204e9800998ecf8427e
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File nameUnique file name of the uploaded fileSmith_m6A_GLORI_seq_rep1_R2.fastq.gz23GCFKLT3_7_R19973_20260116.tar.gz
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File MD5sumMD5sum for the uploaded filea51d8dd983005203e98f09ff8fcf8j27ae