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Studies of homologous recombination in many organisms have shown that mechanisms depending on strand invasion require a minimum length of homology between donor and recipient.
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Single-exon transcripts were oriented to positive strand or negative strand, depending on which strand resulted in higher read counts.
The genes are color coded depending on the strand; genes located on positive strand are black and the ones on negative strand are red.
Slippage error creates a loop in one of the strands that gives rise to an insertion or a deletion in the subsequent replications, depending on the strand specificity (replicating or template strand) of loop formation.
We looked at Alu elements in sense and anti-sense orientation as depending on the strand of integration either one of the two possible orientations can manifest in a transcript.
Conditions for PCR were 95° for 15 min, 50 cycles of 94° for 30 sec, annealing temperature for 30 sec (see Table S3), 72° for 1 min, and finally 72° for 10 min. One forward or reverse primer was biotinylated, depending on which strand contained the target region to be sequenced, to subsequently isolate the strand of interest for pyrosequencing.
Such replication-associated strand bias can potentially result in two classes of genes with distinct nucleotide compositions, depending on which strand they are located.
Depending on the strand's cross section and the casting speed, it can be 10 to 40 metres long.
These four possibilities include the bisulphite-treated reads and their complementary reads (depending on the strand on which the PCR is applied).
A plus or minus was assigned to each synteny anchor depending on the strand where the synteny anchor occured in the NA genome.
A common tag was placed on either the forward or the reverse primer (depending on the strand to be sequenced), and a common universal biotinylated primer was used for all reactions as described previously (44).
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