Reads

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How do I complete the reads manifest for paired-read submission?

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• Ensure that the Reads manifest contains the following:

  • PAIRED as the value for the Library layout column

  • File names in the File name column separated by a comma

  See below for a snapshot of a Reads manifest for paired reads:

  

  Reads manifest for paired reads

Which file types are required for read submissions?

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See the documentation on European Nucleotide Archive (ENA) for details about the types of files that can be submitted for read submissions.

Which reads checklist is linked to samples?

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The reads checklist associated with samples in the dropdown menu on the Reads page is marked with an asterisk (*) and is selected by default when the page loads.

What causes errors during reads updates?

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Hint

The words, manifest and checklist are used interchangeably. They both refer to a spreadsheet.

Errors occur due to several reasons. An error message will be displayed detailing the issue(s) encountered and potential resolution(s). If you are uncertain how to proceed, please contact the .

Updates to reads can be made by uploading the amended manifest to the same checklist and profile initially used for the submission. Please note that this is possible if the values in the Sample, File checksum, File name and Library layout columns remain unchanged in the manifest. If any of these values change, errors will occur during the update process.

This is because the value in the Sample column serves as the key for each row in the Reads manifest. Each unique sample in the manifest corresponds to a different biosample, which is linked to the values in the File checksum, File name and Library layout columns.

Other potential reasons for errors include but are not limited to:

• Uploading null or empty files and associating them with rows in the manifest

• Assigning files to samples that already have the same files attached will produce errors

Are read accessions assigned only after a study is published?

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No, accessions are assigned after reads submissions have been completed.

Publishing a profile (or study) only makes the submissions under the profile public and accessible on repositories such as the European Nucleotide Archive (ENA) and National Centre for Biotechnology Information (NCBI).

See the following sections for more information:

• Finding Data Submission IDs

• Publishing Data

• Where Your Submitted Data Goes

What do the library-related field values mean?

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This section provides a brief overview of library preparation fields and their possible values, including both free-form and controlled vocabulary fields.

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Design description

Goal and setup of the individual library including library was constructed.

Library construction protocol

Free form text describing the protocol by which the sequencing library was constructed.

Library selection

Library selection options

Method used to enrich the target in the sequence library preparation	Description
5-methylcytidine antibody	Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C).
CAGE	Cap-analysis gene expression.
cDNA	PolyA selection or enrichment for messenger RNA (mRNA); synonymise with PolyA
cDNA_oligo_dT	priming by annealing to PolyA tails of eukaryotic mRNAs.
cDNA_randomPriming	random primers typically used to prime mRNAs.
ChIP	Chromatin immunoprecipitation
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.
DNase	DNase I endonuclease digestion and size selection reveals regions of chromatin where the DNA is highly sensitive to DNase I.
HMPR	Hypo-methylated partial restriction digest
Hybrid Selection	Selection by hybridisation in array or solution.
Inverse rRNA	depletion of ribosomal RNA by oligo hybridisation.
Inverse rRNA selection	depletion of ribosomal RNA by inverse oligo hybridisation.
MBD2 protein methyl-CpG binding domain	Enrichment by methyl-CpG binding domain.
MDA	Multiple Displacement Amplification, a non-PCR based DNA amplification technique that amplifies a minute quantifies of DNA to levels suitable for genomic analysis.
MF	Methyl Filtrated
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.
MSLL	Methylation Spanning Linking Library
Oligo-dT	enrichment of messenger RNA (mRNA) by hybridisation to Oligo-dT.
other	Other library enrichment, screening, or selection process.
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).
PCR	target enrichment via PCR
PolyA	PolyA selection or enrichment for messenger RNA (mRNA); should replace cDNA enumeration.
RACE	Rapid Amplification of cDNA Ends.
RANDOM	No Selection or Random selection
RANDOM PCR	Source material was selected by randomly generated primers.
Reduced Representation	Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling.
repeat fractionation	Selection for less repetitive (and more gene rich) sequence through Cot filtration (CF) or other fractionation techniques based on DNA kinetics.
Restriction Digest	DNA fractionation using restriction enzymes.
RT-PCR	target enrichment via
size fractionation	Physical selection of size appropriate targets.
unspecified	Library enrichment, screening, or selection is not specified.

Library source

Library source options

Type of source material being sequenced	Description
GENOMIC	Genomic DNA (includes PCR products from genomic DNA).
GENOMIC SINGLE CELL	Genomic DNA from a single cell.
METAGENOMIC	Mixed material from metagenome.
METATRANSCRIPTOMIC	Transcription products from community targets
OTHER	Other, unspecified or unknown library source material.
SYNTHETIC	Synthetic DNA.
TRANSCRIPTOMIC	Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries).
TRANSCRIPTOMIC SINGLE CELL	Transcriptomic products from a single cell.
VIRAL RNA	Viral RNA.

Library strategy

Library strategy options

Sequencing technique	Description
AMPLICON	Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA .
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.
Bisulfite-Seq	MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status.
ChIA-PET	Direct sequencing of proximity-ligated chromatin immunoprecipitates.
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.
ChM-Seq	ChIPmentation combines chromatin immunoprecipitation with sequencing library preparation by Tn5 transposase
CLONE	Genomic clone based (hierarchical) sequencing.
CLONEEND	Clone end (5’, 3’, or both) sequencing.
CTS	Concatenated Tag Sequencing
DNase-Hypersensitivity	Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI.
EST	Single pass sequencing of cDNA templates
FAIRE-seq	Formaldehyde Assisted Isolation of Regulatory Elements. Reveals regions of open chromatin.
FINISHING	Sequencing intended to finish (close) gaps in existing coverage.
FL-cDNA	Full-length sequencing of cDNA templates
GBS	Genotyping by sequencing is a method to discover single nucleotide polymorphisms for genotyping studies.
Hi-C	Chromosome Conformation Capture technique where a biotin-labelled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing.
MBD-Seq	Methyl CpG Binding Domain Sequencing.
MeDIP-Seq	Methylated DNA Immunoprecipitation Sequencing.
miRNA-Seq	Micro RNA sequencing (miRNA-Seq) is a strategy designed to capture post-transcriptional RNA elements and include non-coding functional elements.
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.
MRE-Seq	Methylation-Sensitive Restriction Enzyme Sequencing.
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).
NOMe-Seq	Nucleosome Occupancy and Methylome sequencing.
OTHER	Library strategy not listed.
POOLCLONE	Shotgun of pooled clones (usually BACs and Fosmids).
RAD-Seq	Restriction site associated DNA marker.
Ribo-Seq	Ribosome profiling (also named ribosome footprinting) that uses specialized messenger RNA (mRNA) sequencing to determine which mRNAs are being actively translated. It produces a “global snapshot” of all the ribosomes active in a cell at a particular moment, known as a translatome.
RIP-Seq	Direct sequencing of RNA immunoprecipitates (includes CLIP-Seq, HITS-CLIP and PAR-CLIP).
RNA-Seq	Random sequencing (RNA-Seq) of whole transcriptome, also known as Whole Transcriptome Shotgun Sequencing (WTSS).
SELEX	Systematic Evolution of Ligands by Exponential enrichment
snRNA-seq	Single nucleus RNA sequencing (snRNA-seq) is a method for profiling gene expression in cells which are difficult to isolate.
ssRNA-seq	Strand-specific RNA sequencing (ssRNA-seq)
Synthetic-Long-Read	binning and barcoding of large DNA fragments to facilitate assembly of the fragment
Targeted-Capture	Enrichment of a targeted subset of loci.
Tethered Chromatin Conformation Capture	Tethered Chromatin Conformation Capture.
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.
VALIDATION	CGHub special request: Independent experiment to re-evaluate putative variants.
WCS	Random sequencing of a whole chromosome or other replicon isolated from a genome.
WGA	Whole Genome Amplification (WGA) followed by random sequencing.
WGS	Whole Genome Sequencing - random sequencing of the whole genome
WXS	Random sequencing of exonic regions selected from the genome.

For a full list of restricted fields and their controlled vocabularies, refer to the experiment attribute list from the European Nucleotide Archive (ENA).

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