Labeling of chromosome paints and genomic DNA and hybridization to the NimbleGen array were performed by the company (NimbleGen) and used a random prime labeling kit to incorporate modified nucleotides by either amino-allyl or direct linkage to either of the two dyes used (Cy3 and Cy5).
cDNA probes corresponding to the mouse C-propeptide of type II collagen (pKN225) [ 16], to 18S rRNA (DECAtemplate 18S mouse; Ambion, Austin, TX, USA), and to the C-terminus of rat aggrecan [ 17, 18] were labeled with [αP]dCTP (3000 Ci/mmol; Perkin Elmer, Woodbridge, ON, Canada) by a random-primed oligonucleotide method (Prime-a-gene labeling kit; Promega).
Where SELEX was primarily used as a tool to analyze the structure of RNA aptamers to a given ligand, Genomic SELEX transforms the method into a discovery tool to screen endogenous RNAs by starting from a pool derived by random priming of the genome of interest.
As there is a 3' end bias in the clone set, a drift away from the poly(A) tail caused by random priming in the second round of amplification could possibly affect the preservation of ratios.
Amplified R and L cDNAs were labelled with [αP] dCTP by random priming (Prime-a-Gene Labelling System, Promega) and used as probes to hybridise zebrafish cDNA commercial libraries: 611 Zebrafish Brain cDNA pt.2 330.1.545, 611 Zebrafish Brain cDNA pt.1 330.1.521 and 609 Zebrafish EST pt.1.357.1.512 (RZPD).
32P-labeled PHO5 upstream and open reading frame probes were prepared by random priming using a 500 bp NotI/BamHI fragment and a 687 bp ScaI/SalI fragment as template, respectively.
By aligning the clustering results, we then compared the expression balance patterns for data obtained by oligo-dT priming with those obtained by random priming for each sense-antisense pair.
The 5S rRNA gene probe, labeled with a32P-dCTP, was generated by random priming of a full-length 5S gene repeat amplified by PCR from clone pCT4.2 [38].
The DNA fragment was labeled with 32P by random priming using a Megaprime DNA labeling kit (GE Healthcare).
