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A poly-adenosine barcode sequence was part of the designed cDNA A1 (cDNA + barcode sequence) to provide a large number of adenine bases for signal amplification.
Novel synthetic MLPA probes were designed to include a unique barcode sequence in each amplified gene.
Furthermore, the forward primer carried an eight-nucleotide barcode sequence between the loop- and the P5-sequence.
A 100% match to both the 12 bp barcode sequence and the partial NgoMIV restriction site were crucial to retain the reads from each sample.
Next, a padlock probe containing a transcript-specific barcode sequence is docked to each ODN and circularized in situ to form a single-stranded DNA circle.
In brief, sequencing reads were de-convoluted on the basis of the used BAC-specific barcode sequence tags and assembled with sequencing centre-specific assembly pipelines.
An indirect analysis strategy for small organic molecules is presented herein, combining aptamer-modified gold nanoparticles (AuNPs) with a designed barcode sequence for amplification.
In order to remove these substitution errors (possibly due to sequencing errors and/or polymerase amplification errors), we clustered the barcode sequence by using our in-house software, Nucleotide Sequence Clusterizer (see Methods).
In the digital counting scheme, typically two types of barcode designs have been used: sequence-restricted barcodes (each barcode sequence is individually designed) and non-sequence-restricted barcodes (occasionally called a "random -base barandom -base
The resulting RCA product (RCP) contains hundreds to thousands of copies of the reverse sequence of the transcript-specific barcode sequence, which is detected using a fluorescently labeled secondary ODN.
This problem is approached by removing errors using computational analyses based on the reasonable assumption that similar barcode sequences generated through errors originated from the same original barcode sequence.
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