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Remaining gaps were closed by sequencing of clones that spanned the gaps or by direct sequencing.
Sea star ParaHox genes are located in a continuous region of 87 kb (depicted in Figure 1B), without any intervening ORFs in between, as determined by sequencing of clones from a P. miniata BAC library.
Prior to the 454 sequencing, a pilot experiment was conducted to analyze the composition of transcripts from both non-normalized and normalized cDNA pools by sequencing of clones from each library.
Bisulfite treatment followed by sequencing of clones showed all 11 CpG sites to be completely unmethylated (see Additional file 1, Figure S2), consistent with active transcription of the 5-exon/4-intron GLTP gene.
Because Taq polymerase had been used in the preparation of the cDNA library and in the generation of the ESTs, the sequence coding for the putative mature protein was confirmed by sequencing of clones derived from RT-PCR products of parasite RNA amplified with Pfu, a DNA polymerase with proofreading activity.
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Gaps between ordered clones or sequence contigs are the second type, which is easily closed by sequencing of bridging clones obtained from pair-end sequence data.
Quantitative methylation analysis of tumour DNA was carried out by cloning bisulfite-PCR products (individual alleles) into pGEM plasmid (Promega, UK) followed by sequencing of individual clones using primers to M13.
Almost no P1 and P2 virus mutations in the Vero and MRC-5 cells grown in T flasks were found by sequencing of multiple clones (Tables 3∼5).
The sequence of linker was confirmed by sequencing of plasmid clones.
In general, these modification rates mimic and support the rates that were obtained by sequencing of individual clones.
Analysis of the mutational spectrum in hESCs by sequencing of PCR clones revealed that mostly deletions as well as few insertions had been introduced by TALEN delivery, like in 293 T cells.
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