SRA library strategy

This document lists the Sequence Read Archive (SRA) library strategies with detailed descriptions.

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.

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)

ChIP-seq is an assay in which chromatin immunoprecipitation with high throughput sequencing is used to identify the cistrome of DNA-associated proteins.

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.