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Sequencing was performed on an ABI 3730 DNA sequencer using BigDye V3.1 (Applied Biosystems) and M13F primer were used for sequencing from the 5' end of cDNAs.
Dorr, C. et al. Differentially expressed gene transcripts using RNA sequencing from the blood of immunosuppressed kidney allograft recipients.
The bottom eight tracks show the TSS activity (blue bars) within the first exons of the different isoforms captured by CAGE sequencing from the FANTOM5 project36,37.
Rather than sequencing from the distal sonication borders as in ChIP-seq, ChIP-exo enriched DNA fragments are sequenced from the left and right 5' DNA borders of the protein-DNA crosslink site.
The resulting 25-bp 5′-cDNA fragments were amplified by 12 cycles of PCR using P1 (5-CCACTACGCCTCCGCTTTCCTCTCTAT-3′) and P2 primers (5′-CTGCCCCGGGTTCCTCATTCT-3′) and were then subject to 25-bp SOLiD single-read sequencing from the P1 sites.
Oligonucleotides complementary to 5′ and 3′ ends of the fragment encoding Kanr were used for initiating nucleotide sequencing from the plus and minus strands of pSP70, and thereafter primer walking was used to determine nucleotide sequence of pSP70.
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Several approaches have been developed to select the regions of interest for sequencing from the genome [20].
Upstream sequencing from the PKS gene using inverse PCR did not indicate any other recognizable copy of this gene was nearby.
Moreover, recent sequencing from the B73 inbred line has revealed a P1-wr allele with eleven similar tandemly-arranged copies [20].
E. coli carrying clones from each of the cDNA libraries were robotically processed, including: plating, colony picking, growth in 96 well format, plasmid isolation, and random sequencing from the 5' end via dideoxy sequencing.
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