Table 1.
Plasmid, BAC, and fosmid DNA libraries sequenced in a 400-nL reaction containing 31.25 nL of Big Dye terminators (V3.1, Applied Biosystems) as compared to standard 4000-nL reactions containing 540 nL of Big Dye terminators
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|
|
|
|
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|
|
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31.25 nL Big Dye |
540 nL Big Dye |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sequence type |
Organism |
Library name |
Vector |
Vector copy number |
Mean insert size (kbp) |
GC content |
DNA conc. (mean ± SD) (ng/μL) |
Primer |
Number of reads |
Length (PHRED20 bp, mean ± SD) |
Mean signal strength |
Length (PHRED20 bp, mean ± SD) |
Mean signal strength |
||
| 5′ EST | H. sapiens | 10790a | pOTB7 | High | 1.9 | N/A | 70.31 ± 0.89 | -21M13F | 2304 | 881 ± 72 | 1072 | 879 ± 100 | 1053 | ||
| 5′ EST | M. musculus | LL005, LL012, LL014, LL015, LL016, LL017 | pDNRLIB | High | 2.3 | 51% | 47.87 ± 2.19 | -21M13F, T7 | 2230 | 738 ± 189 | 342 | 753 ± 200 | 1987 | ||
| R. norvegicus | pYX-Asc | ||||||||||||||
| H. sapiens | pOTB7 | ||||||||||||||
| X. tropicalis | pCMV-SPORT6 | ||||||||||||||
| SAGE | H. sapiens (prostate cancer) | S1881 | pZero-1 | High | 0.834 | 47% | 30.42 ± 0.82 | T7 | 2281 | 764 ± 157 | 381 | 786 ± 156 | 1169 | ||
| WGS | Cryptococcus neoformans | CN23E | pBR194cE | Medium | 10 | 47% | 15.17 ± 0.19 | -21M13F | 2304 | 715 ± 171 | 104 | 825 ± 142 | 593 | ||
| Transposonb | Xenopus laevis | TX060, TX067 | pCMV-SPORT6 | High | 3.4c | 45% | 72.38 ± 2.63 | SeqA2 | 1152 | 740 ± 170 | 333 | 774 ± 242 | 3190 | ||
| Fosmid end | Chlamydia trachomatis | CA000, CD000, CE000, CL000 | pEpiFos5 | Low | 30 | 42% | 40.52 ± 0.60 | pEpiFos5 Forward | 1824 | 621 ± 201 | 255 | N/A | N/A | ||
| BAC end
|
Gasterosteus aculeatus
|
GA000
|
pTarBAC2.1
|
Low
|
210
|
43%
|
50.76 ± 0.87
|
T7
|
568
|
646.97 ± 189
|
199
|
N/A
|
N/A
|
||
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↵a Library 10790 is comprised of multiple copies of an identical clone
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↵b Transposons carrying unique priming sites are randomly inserted by recombination into pooled sets of plasmid clones (Butterfield et al. 2002)
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↵c Includes 2.3 kb of insert plus 1.1 kb transposon
