Library strategy

This document lists the accepted library strategies for read domain experiment submissions, with detailed descriptions of each.

POOLCLONE

Pooled clone sequencing: An assay in which DNA is the input molecule derived from pooled clones (for example BACs and Fosmids) is sequenced using high throughput technology using shotgun methodology.

CLONE

Clone by clone sequencing: An assay in which DNA is the input molecule derived from clones which are mapped then sequenced in small fragments.

CLONEEND

Clone end sequencing: An Assay in which DNA is the input molecule derived from a clone and 5',3' or both ends of a clone are sequenced.

WGS

Whole genome shotgun sequencing: An assay in which DNA is the input molecule derived from fragmented whole genome preparation is sequenced.

WGA

Whole genome amplification sequencing: Non-PCR amplification of the whole genome, followed by random sequencing.

WCS

Random chromosome sequencing: An assay in which DNA is the input molecule derived from chromosome or other replicon is sequenced.

WXS

Random exon sequencing: An assay in which DNA is the input molecule derived from exons is sequenced.

AMPLICON

Amplicon sequencing: An assay in which a DNA or RNA input molecule amplified by PCR is sequenced.

ChIP-Seq

Direct sequencing of chromatin immunoprecipitates: An assay in which chromatin immunoprecipitation with high throughput sequencing is used to identify the cistrome of DNA-associated proteins.

RNA-Seq

Whole Transcriptome Shotgun Sequencing: Random sequencing of whole transcriptome, also known as Whole Transcriptome Shotgun Sequencing, or WTSS.

MRE-Seq

Methylation-Sensitive Restriction Enzyme Sequencing strategy: An assay in which DNA is the input molecule derived from cleavage of DNA by use of methylation sensitive restriction enzymes to fragment DNA at methylation sites before sequencing.

MeDIP-Seq

Methylated DNA Immunoprecipitation Sequencing strategy: An assay in which DNA is the input molecule derived from an antibody based selection process using antibodies targeting methylated DNA, which is then sequenced using high throughput sequencing technology.

MBD-Seq

Direct sequencing of methylated fractions sequencing strategy: An assay in which DNA is the input molecule derived from a selection process using methyl binding domain protein to enrich for methylated fractions of DNA, then sequenced using high throughput sequencing.

MNase-Seq

Direct sequencing following MNase digestion: An assay in which DNA is the input molecule derived from a micrococcal nuclease digestion followed by high throughput sequencing, A method that distinguishes nucleosome positioning based on the ability of nucleosomes to protect associated DNA from digestion by micrococcal nuclease. Sequenced fragments reveal nucleosome location information about the input DNA.

DNase-Hypersensitivity

Sequencing of DNase-hypersensitive sites to identify regularatory elements: An assay in which DNA is the input molecule derived from a DNase-hypersensitivity digest of chromatin with the aim of identifying regulatory elements.

Bisulfite-Seq

Sequencing following treatment of DNA with bisulfite to determine methylation status: An assay in which DNA is the input molecule derived from a bisulphite treatment of DNA to convert cytosine residues to uracil to determine methylation status.

EST

Single pass sequencing of cDNA templates: An assay in which RNA derived from an Expressed Sequence Tags (ESTs) is sequenced.

FL-cDNA

Full-length sequencing of cDNA templates: An assay in which RNA derived from a full length cDNA template is sequenced.

miRNA-Seq

Micro RNA sequencing: Micro RNA sequencing strategy designed to capture post-transcriptional RNA elements and include non-coding functional elements

ncRNA-Seq

Non-coding RNA sequencing: 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)

FINISHING

Sequencing intended to finish (close) gaps in existing coverage.

CTS

Concatenated Tag Sequencing.

Tn-Seq

Transposon RNA sequencing: 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. Gene fitness determination through transposon seeding.

VALIDATION

Validation sequencing: CGHub special request. Independent experiment to re-evaluate putative variants. Micro RNA sequencing strategy designed to capturepost-transcriptional RNA elements and include non-coding functional elements.

FAIRE-seq

Formaldehyde Assisted Isolation of Regulatory Elements sequencing: Used for determining the sequences of those DNA regions in the genome associated with regulatory activity.

SELEX

Systematic Evolution of Ligands by EXponential enrichment sequencing: An assay involving progressive selection of oligonucleotides with certain affinities to target molecules.

RIP-Seq

RNA-immunoprecipitation sequencing: Direct sequencing of RNA immunoprecipitates (includes CLIP-Seq, HITS-CLIP and PAR-CLIP).

ChIA-PET

Chromatin Interaction Analysis by Paired-End Tag sequencing: Direct sequencing of proximity-ligated chromatin immunoprecipitates.

RAD-Seq

Restriction site Associated DNA sequencing: A method for sampling the genomes of multiple individuals in a population using next generation DNA sequencing.

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