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Glossary
Replicate A repetition of the same experimental measurement. The replicate can
either be technical, where the same biological extract is analyzed twice, e.g. by using
the same mRNA for multiple microarrays; or it can be a biological replicate, when
for example sample material is harvested from different individuals grown under the
same conditions.
Reporter/Probe An oligonucleotide attached to the surface of a microarray.
RNA interference (RNAi) a genetic mechanism in which double-stranded
RNA is cleaved into small fragments and acts a signal to either initiate
the degradation of a complementary messenger RNA or to interfere with its
translation.
ROS Reactive Oxygen species; Small molecules or ions formed by the incomplete one-electron reduction of oxygen; ROS contribute to oxidative stress/damage
of DNA, lipids (oxidations of polydesaturated fatty acids), proteins (oxidations of
amino acids) and inactivate specific enzymes (oxidation of co-factors).
SAGE Serial Analysis of Gene Expression. A high-throughput method to measure gene-expression by sequencing. Short fragments (tags) are generated from
cDNA, which are then ligated to form long concatenated sequences, and
sequenced.
Seaweed Brown, red or green macroalgae.
Scatter-plot A two-dimensional plot where each measurement value is depicted by
a single dot. Scatter-plots are often used to inspect data distributions.
SDS-PAGE Sodium dodecylsulphate – polyacrylamide gel electrophoresis;
method used to separate proteins involving electrophoresis on an acrylamide gel.
Secondary endosymbiosis An event in which a eukaryotic cell enslaves another
eukaryotic cell that possesses a plastid derived from a primary endosymbiosis (see
also endosymbiosis and primary endosymbiosis).
Sequence trace file Raw sequence data in the form of a chromatogram from a
Sanger sequencing reaction. The NCBI Trace Archive (http://www.ncbi.nlm.
nih.gov.gate1.inist.fr/Traces/home/)
and
the
Ensembl
Trace
Server
(http://trace.ensembl.org/) are a public repositories for this sort of data.
Short Read Archive (SRA) An NCBI database that stores raw data from sequencing platforms such as the Roche 454 System.
Singleton A single EST sequence that does not cluster with other ESTs.
SNP Single-nucleotide polymorphism; particular sites (base pairs) in a sequence
that are polymorphic and can be used as markers.
SOM Self Organizing Maps.
Sporophyte A spore-producing plant.
Glossary
Replicate A repetition of the same experimental measurement. The replicate can
either be technical, where the same biological extract is analyzed twice, e.g. by using
the same mRNA for multiple microarrays; or it can be a biological replicate, when
for example sample material is harvested from different individuals grown under the
same conditions.
Reporter/Probe An oligonucleotide attached to the surface of a microarray.
RNA interference (RNAi) a genetic mechanism in which double-stranded
RNA is cleaved into small fragments and acts a signal to either initiate
the degradation of a complementary messenger RNA or to interfere with its
translation.
ROS Reactive Oxygen species; Small molecules or ions formed by the incomplete one-electron reduction of oxygen; ROS contribute to oxidative stress/damage
of DNA, lipids (oxidations of polydesaturated fatty acids), proteins (oxidations of
amino acids) and inactivate specific enzymes (oxidation of co-factors).
SAGE Serial Analysis of Gene Expression. A high-throughput method to measure gene-expression by sequencing. Short fragments (tags) are generated from
cDNA, which are then ligated to form long concatenated sequences, and
sequenced.
Seaweed Brown, red or green macroalgae.
Scatter-plot A two-dimensional plot where each measurement value is depicted by
a single dot. Scatter-plots are often used to inspect data distributions.
SDS-PAGE Sodium dodecylsulphate – polyacrylamide gel electrophoresis;
method used to separate proteins involving electrophoresis on an acrylamide gel.
Secondary endosymbiosis An event in which a eukaryotic cell enslaves another
eukaryotic cell that possesses a plastid derived from a primary endosymbiosis (see
also endosymbiosis and primary endosymbiosis).
Sequence trace file Raw sequence data in the form of a chromatogram from a
Sanger sequencing reaction. The NCBI Trace Archive (http://www.ncbi.nlm.
nih.gov.gate1.inist.fr/Traces/home/)
and
the
Ensembl
Trace
Server
(http://trace.ensembl.org/) are a public repositories for this sort of data.
Short Read Archive (SRA) An NCBI database that stores raw data from sequencing platforms such as the Roche 454 System.
Singleton A single EST sequence that does not cluster with other ESTs.
SNP Single-nucleotide polymorphism; particular sites (base pairs) in a sequence
that are polymorphic and can be used as markers.
SOM Self Organizing Maps.
Sporophyte A spore-producing plant.