ABCDEFGHIJKLMNOPQRSTUVWXYZ
1
Metadata sheet per SampleDescriptionExampleYour sample details
2
3
All fields marked with * are mandatory. Enter your details in column E.
4
Example values for each field is provided in column D for aid with filling the sheet.
5
Make edits only in column E. Do not change the field names.
6
7
Enter information and contact details of the lab, PI and submitter in submission information fields.
8
9
Submission InfoPlatform*Sequencing platformONT
10
Project ID*Unique ID associated to all the samples of this submissionSmith_rRNA
11
Submission date*Date when sequencing data were upload10/25/2025
12
Submission author*Person doing the submissionJane Doe
13
Submission author email*Email from person doing the submissionjane.doe@university.edu
14
Laboratory head/PI*PI's last nameSmith
15
Contact email*PI's email or other contact emailj.smith@university.edu
16
17
Sample RNASample name*Unique sample name associated to your submissionNovoa_rRNA_native_rep1
18
Sample type*RNA biotyperRNA
19
Sample description*Description of the sample being processedTotal RNA was DNAse-treated, in vitro
polyadenylated using Ecoli PAP, and prepared
for nanopore direct RNA sequencing using
following manufacturer's recommendations
20
RIN value*RIN value of sample prior to starting library prep9.1
21
Replicate information*Replicate number (total number of replicates)Rep1 (of 3)
22
23
Enter information related to library and library preparation method.
24
25
Library preparationLibrary preparation protocol version*ONT library preparation protocol version usedDRS_9195_v4_revI_30Jul2025
26
Variations to the protocolAny variations that are not described
in the protocol version mentioned above		Maxima RT enzyme instead of SSIV
27
Device used to measure RIN*Device used to obtain RIN valueTapeStation
28
RNA input*Input amount used to start the library300ng
29
Kit name*Library prep kitSQK-RNA004
30
Multiplexing*Was your run multiplexed? (yes/no)Yes
31
Multiplexing barcodeBarcode and model used for demultiplexingb04_RNA004 - barcode1 (SeqTagger)
32
Barcode sequence (if not standard RLA)If any additional adapters /multiplexing adapters were usedNA
33
Library mass loaded*Amount of library loaded (based on cDNA measurement)50ng
34
35
Enter information related to the sequencing instrument and read statistics.
36
37
Sequencing SettingsSequencing run ID*Your unique runID used in MinKNOW configP2_RNA250924_rRNA_native_rep1
38
Instrument type*Device used for sequencing PromethION
39
Flow cell type*MinION/PromethION flowcell typeFLO-MIN106D
40
Flow cell ID*Unique flowcell IDFAK23441
41
Flowcell re-use*Had this flowcell been previously used for another run? (yes/no)Yes
42
Available pores at start of sequencing*Number of pores available at start 1500
43
Sequencing script usedIf any variations to MinKNOW config.toml were usedDefault
44
MinKNOW version*MinKNOW software version25.6.8
45
Date sequenced*Sequencing start date9/24/2025
46
Sequencing run timeTime for which the sample was sequenced72h
47
48
Sequencing outputNumber of raw reads of the run*Number of sequenced reads of the run1000000
49
Number of demuxed reads of the run*Number of demuxed reads (for all samples in the flowcell)990000
50
Number of demuxed reads of YOUR SAMPLE*Number of demuxed reads corresponding to THIS SAMPLE250000
51
Number of basecalled reads of YOUR SAMPLE*Number of basecalled reads (if multiplexed, only specify basecalled
reads of your sample, not of the total run)		249000
52
Median Q score*Q score of the sequencing run14.2
53
N50*N50 value provided by MinKNOW1500
54
55
Data analysisBasecalling software*Software used for basecallingDorado
56
Basecalling software version*Version of the basecalling software5.1.0
57
Basecalling software parameters*Parameters used during basecalling step--min-qscore 10 --reference ~/scratch/ref/chm13v2.0.fa.gz --modified-bases pseU_2OmeU inosine_m6A_2OmeA 2OmeG m5C_2OmeC --estimate-poly-a sup
58
Demultiplexing software Software used for demultiplexiingSeqTagger
59
Demultiplexing software versionVersion of the demultiplexing software1.1
60
Demultiplexing software parametersParameters used during demuxing stepNA
61
Demultiplexing modelModel used for demuxingb04_RNA004
62
Mapping software*Software used for mappingMinimap2
63
Mapping software version*Version of the mapping software2.17
64
Mapping software parameters*Parameters used during mapping step -ax map-ont
65
66
Modification data analysisModification-aware model (yes/no)*Please write YES/NO if modification-aware model was used YES
67
Dorado Modification-aware model - specifyUsing the nomenclature from ONT doradopseU
68
If other methods were used for predicting
modifications, please specify software and version		Custom software names used to detect modificationsNanoRMS4 version 1.0
69
If other modifications were predicted using
non-ONT dorado models, specify which ones		Please write the modificationsPseudouridine
70
71
Enter information about the file name and md5sum of the uploaded files.
72
If more files are to be uploaded, add rows below.
73
74
FileRaw data file name*File name containing the raw reads in POD5 formatP2_RNA250924_rRNA_native_rep1.tar.gz
75
Raw data MD5sum*Unique md5sum for your data to ensure that
the data upload/download is complete		o41d8cd98f00b204e9800998ecf8427e
76
Basecalled data file name*File name containing the basecalled reads in FASTQ.GZ formatP2_RNA250924_rRNA_native_rep1.fastq.gz
77
Basecalled data MD5sum*Unique md5sum for your data to ensure that
the data upload/download is complete		x41d8cd98f00b204e9800998ecf8427e
78
Mapped data file name*File name containing the mapped reads in BAM formatP2_RNA250924_rRNA_native_rep1.BAM.gz
79
Mapped data MD5sum*Unique md5sum for your data to ensure that
the data upload/download is complete		a41d8cd98f00b204e9800998ecf8427e
80
Predicted modifications and stoichiometries*File name containing the predicted modified sites and
stoichiometries in BEDMETHYL format, please specify the MOD TYPE in the NAME		P2_RNA250924_rRNA_native_rep1_dorado_pseU.bedmethyl.gz
81
Predicted modifications md5sum*Unique md5sum for your data to ensure that
the data upload/download is complete		d41d8cd98f00b204e9800998ecf8427e
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100