Edinburgh/Notebook/Minipreps

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== Minipreps of Confirmed Clones ==

* '''M2:''' pSB1A2+dxs
* '''M15:''' pSB1A2+appY
* '''(?) M36:''' pSB1A2+crtB (sequencing results not recorded, but follow-up did occur)
* '''(?) M42:''' pSB1A2+crtI (sequencing results not recorded, but follow-up did occur)
* '''M43:''' BABEL2(?)+glgC double mutant.
* '''M50:''' pSB1A2+rbs+crtI
* '''M63:''' BABEL2+rbs+crtE
* '''M67:''' pSB1A2+rbs+crtB
* '''M72:''' pSB1A2+rbs+dxs
* '''M79:''' BABEL2+crtE
* '''M82:''' pSB1A2+rbs+appY
* '''M109:''' pSB1A2+crtBI
* '''(?) M121:''' pSB1A2+CrtY (sequencing results not posted; no follow-up recorded)
* '''(?) M124''' pSB1A2+rbs+CrtY (sequencing results not posted; no follow-up recorded)
* '''M116:''' pSB1A2+glgC double mutant
* '''M130:''' pSB1A2+PcstA
* '''M137:''' pSB1A2+dxs+lims
* '''M150:''' pSB1A2+cex
* '''M152:''' pSB1A2+dxs+crtE
** '''M154:''' not sequenced, but similar to M152.
** '''M155:''' not sequenced, but also similar to M152; ligated to M110 (CrtBI) in L62.
* '''M162:''' pSB1A2+dxs+lims+appY
* '''M212:''' pSB1A2+glgC triple mutant (ie, ''glgC16'')
* '''M222:''' pSB1A2+Plac+''dxs+LIMS1+appY''
* '''M233:''' pSB1A2+cex mutant (PstI site removed)
** '''M234, 235:''' not sequenced, but similar to M233.
* '''M237, 238:''' pSB1A2+cenA
* '''M243:''' pSB1A2+rbs+glgC
* '''M245:''' pSB1A2+rbs+glgC16
* '''M254:''' pSB1A2+Plac+rbs+''glgC''
* '''M256:''' pSB1A2+Plac+rbs+''glgC16''
* '''M258:''' pSB1A2+PcstA+''lacZ' '' (BBa_J15202)
* '''M259:''' pSB1A2+PcstA+''xylE'' (BBa_J33204)
* '''M281:''' pSB1A2+''bglX'' coding sequence
* '''M303:''' pSB1A2+rbs+''cex''
* '''M305:''' pSB1A2+rbs+''cenA''
* '''M307:''' pSB1A2+rbs+''bglX''

== Complete List of Minipreps ==

'''M1 to M6:''' pSB1A2+''dxs'' transformants (plate 11). M2, M3, M4 and M6 all looked correct on gel 2. (30.06.08) - M2 was sequenced to confirm identity and was maxiprepped as '''X2'''.<br />
'''M7:''' BABEL1+''glgC'' transformant (plate 12). Did not look right on gel. (30.06.08)<br />
'''M8 to M12:''' BABEL2+''glgC'' transformants (plate 13). M10 and M11 both looked good on a gel, but sequencing showed that both had the insert in the reverse orientation. (30.06.08)<br />
'''M13 to M18:''' pSB1A2+''appY'' transformants. Gel 10 showed that M15 to M18, and possibly M14, all seemed to have inserts the right size. (09.07.08)<br />
'''M19 to M24:''' BABEL2+''glgC'' clones after mutation of EcoRI site 2. EcoRI digests on *Gel 11* suggest that *M19, M21 and M22* may have lost the EcoRI site. (10.07.08)<br />
'''M25 to M30:''' possible rbs+''dxs'' transformants from plate 34. (13.07.08)<br />
'''M31 to M36:''' pSB1A2+''crtB'' clones from plate 35. (14.07.08)<br />
'''M37 to M42:''' pSB1A2+''crtI'' clones from plate 36. (14.07.08)<br />
'''M43 to M47:''' possible BABEL2+''glgC'' double mutants (both EcoRI sites gone). (19.07.08)<br />
'''M48:''' a possible pSB1A2+rbs+''dxs'' clone. (19.07.08)<br />
'''M49 to M54:''' pSB1A2-rbs+''crtI''. (29.07.08: CF)<br />
'''M55 to M60:''' Putative pSB1A2+pZntA (L23). (29.07.08: Yan, Nimisha) - M50 sequenced (31.07.08: CF)<br />
'''M61 to M66:''' Putative pSB1A2+rbs+''crtE'' (L22). (29.07.08: Yan, Nimisha) - M63 sequenced (31.07.08: CF)<br />
'''M67:''' rbs+''crtB'' (L21) (29.07.08: Yan, Nimisha) - Sequenced (31.07.08: CF)<br />
'''M68 to M71:''' pSB1A2+''glgC''-mut1,2 from plate 73 (31.07.08: AM, Yan)<br />
'''M72 to M75:''' pSB1A2+rbs+''dxs'' from plate 74 (31.07.08: AM, Yan)<br />
'''M76 to M79:''' BABEL2+''crtE'' from plate 74 (31.07.08: AM, Yan)<br/>
'''M80 to M83:''' pSB1A2+rbs+''appY'' from plate 83. (04.08.08: Yan, OG)<br />
'''M84 to M85:''' pSB1A2+rbs+''crtB'' from plate 84. (04.08.08: Yan, OG)<br />
'''M86 to M90:''' pSB1A2+''cenA'' from plate 85. (04.08.08: Yan, OG)<br />
'''M91 to M96:''' pSB1A2+''cex'' from plate 86. (04.08.08: Yan, OG)<br />
'''M97 to M104:''' pSB1A2+''cenA'' from plate 85. (05.08.08: Yan)<br />
'''M105 to M108:''' pSB1A2+''cex'' from plate 85. (05.08.08: Yan)<br />
'''M109 to M112:''' pSB1A2+''crtB''+''crtI'' and plate 102 (11.08.08: OG)<br />
'''M113 to M116:''' pSB1A2+''glgC''-mut1,2 and plate 103 (11.08.08: OG)<br />
'''M117 to M120:''' pSB1A2+''glgC''-mut1,2,3 and plate 94 (11.08.08: OG)<br />
'''M121 to M123:''' pSB1A2-crtY (12.08.08: OG)<br />
'''M124 to M126:''' pSBA12-rbs+crtY (12.08.08: OG)<br />
'''M127 to M130:''' pSB1A2-PcstA from plate 115 (13.08.08: OG)<br />
'''M131 to M134:''' Minipreps of dxs+crtE (1,2,3,4) Note: M132 might be M136 (13.08.08: OG)<br />
'''M135 to M138:''' Minipreps of dxs+lims (1,2,3,4) Note: M136 might be M132 (13.08.08: OG)<br />
'''M139 to M143:''' Minipreps of pSB1A2 +CrtE (1 to 4) Note: M142 and M143 both made from culture 4.(15.08.08: YAN/OG)<br />
'''M144 to M147:''' pSB1A2+cenA from plate 129 - Methanol used in preparation rather than ethanol! (18.08.08: OG)<br />
'''M148 to M151:''' pSB1A2+cex from plate 129. (18.08.08: OG)<br />
'''M152 to M155:''' pSB1A2+dxs+crtE from plate 130 (18.08.08: OG)<br />
'''M156 to M159:''' pSB1A2+cenA (20.08.08: OG)<br/>
'''M160 to M163:''' Plate 155 streaks 1-4 (L48, pSB1A2+dxs+lims+appY) (25.08.08: AH)<br/>
'''M164''': Plate 155 streak 5 (L49, pSB1A2+crtB+crtI+appY) (25.08.08: AH)<br/>
'''M165 to M168:''' Plate 158 streaks 1-4 (L50, SOB+glgC-mut1,2) (25.08.08: AH)<br/>
'''M169 to M172:''' Plate 159 streaks 1-4 (L51, SOB+glgC-mut1,2,3) (25.08.08: AH, Yan)<br/>
'''M173:''' Plate 160 streak 1 (L55 (SOB+rbs+glgC-mut1,2,3) (25.08.08: Yan)<br/>
'''M174 to M175:''' Plate 160 streaks 2 and 3 (L52, SOB+glgC-mut1,2,3) (25.08.08: Yan)<br/>
'''M176 to M178:''' Plate 161 streaks 1-3 (L53, SOB+rbs+glgC-mut1,2) (25.08.08: Yan)<br/>
'''M179 to M181:''' Plate 163 streaks 1-3 (L56, pSB1A2+pCstA+lacZ') (25.08.08: Yan)<br/>
'''M182 to M187:''' pSB1A2+CenA (01.09.08: YAN)<br/>
'''M188 to M193:''' CrtBI+AppY (01.09.08: YAN)<br/>
'''M194 to M197:''' AppY+dxs+Lims (02.09.08:YAN)<br/>
'''M198 to M200:''' L58 = self-ligation of P91 (SOB2-zm1). M199 and M200 were missed out by accident. (09.09.08: Yan)<br/>
'''M201 to M203:''' L59 = self-ligation of P92 (SOB2-rbs-zm1). (09.09.08: Yan)<br/>
'''M204 to M206:''' L60 = self-ligation of P93 (SOB2-zm2). (09.09.08: Yan)<br/>
'''M207 to M209:''' L61 = self-ligation of P94 (SOB2-rbs-zm2). (09.09.08: Yan)<br/>
'''M210 to M212:''' pSB1A2-glgc triple mutants. (15.09.08: AM)<br/>
'''M213:''' dxs+CrtEBI. (15.09.08: AM)<br/>
'''M214:''' pSB1A2-CenA. (15.09.08: AM)<br/>
'''M215 to M216:''' pSB1A2-bglX. (15.09.08: AM)<br/>
'''M217 to M221:''' dxs+crtEBI. (15.09.08: AM)<br/>
'''M222 to M225:''' Plac+dxs+LIMS1+appY patches 1, 2, 6 and 7 (CF, 23-9-8). All look OK on gel. M222 confirmed by sequencing.<br/>
'''M226 to M229:''' SOB-ZmISA1. (CF, 27-9-8) Only M229 looks plausible on gel, but sequencing shows problem at end. <br/>
'''M230 to M232:''' SOB-ZmISA2. (CF, 27-9-8) All looked OK; sequencing showed M230 and 232 OK, 231 problem with suffix.<br/>
'''M233 to M235:''' pSB1A2-cex mutant (CF) Sequence showed M233 OK.<br/>
'''M236 to M238:''' pSB1A2-cenA (CF, 27-9-8) . M236 clearly wrong on gel, others plausible. Sequence showed M237 OK.<br/>
'''M239 to M241:''' pSB1A2-bglX (CF, 27-9-8) Only 240 looked plausible on gel, sequence showed wrong.<br/>
'''M242 to M243:''' pSB1A2-rbs-glgC (CF, 28-9-8)<br/>
'''M244 to M245:''' pSB1A2-rbs-glgC16 (CF, 28-9-8)<br/>
'''M246 to M247:''' pSB1A2-bglX (CF, 28-9-8). M247 looks plausible but sequencing shows wrong. <br/>
'''M248 to M253:''' pSB1A2-crtBI-dxs-crtE (CF, 30-9-8). All look wrong.<br/>
'''M254 to M255:''' pSB1A2-Plac-glgC (CF, 2-10-8). Look OK. M254 confirmed by sequencing.<br/>
'''M256 to M257:''' pSB1A2-Plac-glgC16 (CF, 2-10-8). Look OK. M256 confirmed by sequencing.<br/>
'''M258:''' pSB1A2-PcstA-lacZ' (CF, 2-10-8). Looks OK, confirmed by sequencing.<br/>
'''M259:''' pSb1A2-PcstA-xylE (CF, 2-10-8). Looks OK, confirmed by sequencing.<br/>
'''M260 to M265:''' SOB-ZmISA1 (CF, 3-10-8). M265 looks OK on gel, confirmed by sequencing.<br/>
'''M266 to M269:''' SOB-ZmISA2 (CF, 4-10-8). M269 looks plausible on gel.<br/>
'''M270 to M272:''' pSB1A2+rbs+cex (CF, 8-10-8). All look wrong.<br/>
'''M273 to M275:''' pSB1A2+rbs+cenA (CF, 8-10-8). M273, 274 looked OK but turned out to be wrong gene.<br/>
'''M276 to M278:''' pSB1A2+rbs+cex (CF, 11-10-8). M276 looked OK but turned out to be wrong gene.<br/>
'''M279 to M282:''' pSB1A2+bglX (CF, 14-10-8). All looked Ok on gel, but sequencing showed that all but M281 had frameshift mutations in a run of A near the start resulting in premature termination. M281 seems OK though.<br/>
'''M283 to M286:''' from mutagenesis of ZmISA1 (CF, 14-10-8 and 15-10-8). M286 looks wrong, others still seem to have the EcoRI site.<br/>
'''M287 to M290:''' from mutagenesis of ZmISA2 (CF, 15-10-8). All seem to still have EcoRI site.<br/>
'''M291 to M293:''' pSB1A2+Plac+crtBI (CF, 16-10-8). All look OK.<br/>
'''M294 to M296:''' pSB1A2+Plac+dxs.crtE (CF, 16-10-8). All look OK.<br/>
'''M297 to M300:''' from mutagenesis of ZmISA1 (CF, 19-10-8). All seem to still have EcoRI site.<br/>
'''M301:''' from mutagenesis of ZmISA2 (CF, 19-10-8). Seems to still have EcoRI site.<br/>
'''M302:''' supposed to be Plac+dxs.crtEBI but seems to be just Plac+dxs.crtE (CF, 19-10-8).<br/>
'''M303 to M304:''' pSB1A2+rbs+cex (CF, 26-10-8). Both look OK.<br/>
'''M305 to M306:''' pSB1A2+rbs+cenA (CF, 26-10-8). Both look OK.<br/>
'''M307 to M308:''' pSB1A2+rbs+bglX (CF, 26-10-8). Both look OK.<br/>