Ryan Quan's notebook

From 2009.igem.org

(Difference between revisions)
Line 14: Line 14:
-miniprepped cultures for 1,3,4,5,6,8
-miniprepped cultures for 1,3,4,5,6,8
 +
-sent in sample for sequencing
-sent in sample for sequencing
'''9/28/09'''
'''9/28/09'''
 +
-ran gel for PCRs
-ran gel for PCRs
 +
-set up cultures for 1,3,4,5,6,8
-set up cultures for 1,3,4,5,6,8
'''9/25/09'''
'''9/25/09'''
 +
-Set up PCR for biobrick parts 2 and 9 with elongase
-Set up PCR for biobrick parts 2 and 9 with elongase
'''9/18/09'''
'''9/18/09'''
 +
-ran PCR again for 2 and 9 using KOD
-ran PCR again for 2 and 9 using KOD
 +
-ran gel for PCR
-ran gel for PCR
'''9/11/09'''
'''9/11/09'''
 +
-ran gel again for PCRs
-ran gel again for PCRs
'''9/9/09'''
'''9/9/09'''
 +
-ran a gel for PCRs
-ran a gel for PCRs
 +
-set up BPGW for PCRs
-set up BPGW for PCRs
 +
-xformed into dh5alpha
-xformed into dh5alpha
'''9/4/09'''
'''9/4/09'''
 +
-set up PCR for biobricks
-set up PCR for biobricks
 +
-DPN1 treated
-DPN1 treated
 +
-PCR purified
-PCR purified
'''8/26/09'''
'''8/26/09'''
 +
-set up test digest for ligations of 347-92,93 and FRB-FKBP-FKBP
-set up test digest for ligations of 347-92,93 and FRB-FKBP-FKBP
 +
-ran a gel for test digests
-ran a gel for test digests
8/21/09'''
8/21/09'''
 +
-made movies of ho46,320,331,332,333,334,335
-made movies of ho46,320,331,332,333,334,335
'''8/19/09'''
'''8/19/09'''
 +
-set up cultures for ligations of pho347-93,92 and FRB-FKBP-FKBP
-set up cultures for ligations of pho347-93,92 and FRB-FKBP-FKBP
'''8/13/09'''
'''8/13/09'''
 +
-heat inactivated Aar1 digest
-heat inactivated Aar1 digest
 +
-ran gel for digest
-ran gel for digest
 +
-gel purified
-gel purified
 +
-set up ligations for pho347 w/ 92,93 and AB FRB, BC FKBP, CD FKBP
-set up ligations for pho347 w/ 92,93 and AB FRB, BC FKBP, CD FKBP
'''8/12/09'''
'''8/12/09'''
 +
-miniprepped pho347
-miniprepped pho347
 +
-set up Aar1 digest of pho347 o/n
-set up Aar1 digest of pho347 o/n
'''8/11/09'''
'''8/11/09'''
 +
-miniprepped LR cultures
-miniprepped LR cultures
 +
-sent in for sequencing (LRs)
-sent in for sequencing (LRs)
 +
-made movie of ho46,320,331,332,333,334
-made movie of ho46,320,331,332,333,334
 +
-set up culture for pho347
-set up culture for pho347
'''8/10/09'''
'''8/10/09'''
 +
-froze ho335,336
-froze ho335,336
 +
-set up cultures for LRs of pho203-pho275 to pho203-pho382
-set up cultures for LRs of pho203-pho275 to pho203-pho382
 +
-xformed pho347 for plasmid amp
-xformed pho347 for plasmid amp
'''8/7/09'''
'''8/7/09'''
 +
-made movies of ho46,180,181,182,227
-made movies of ho46,180,181,182,227
 +
-checked sequences
-checked sequences
'''8/6/09'''
'''8/6/09'''
 +
-sent in samples for sequencing from 8/5/09 test digest
-sent in samples for sequencing from 8/5/09 test digest
 +
-set up LR rxn for pho375,376,377,378,379,380,381
-set up LR rxn for pho375,376,377,378,379,380,381
'''8/5/09'''
'''8/5/09'''
 +
-set up LRGW for good clones of ligations
-set up LRGW for good clones of ligations
 +
-froze ho46 w/ pho304 --ho3
-froze ho46 w/ pho304 --ho3
 +
-miniprepped cltures from 8/4/09
-miniprepped cltures from 8/4/09
 +
-set up test digest for minipreps
-set up test digest for minipreps
 +
-ran a gel for test digests
-ran a gel for test digests
'''8/4/09'''
'''8/4/09'''
 +
-set up for movies of ho46,179,180,181,182,227
-set up for movies of ho46,179,180,181,182,227
 +
-set up cultures for 347-50-60-92-93-143-353
-set up cultures for 347-50-60-92-93-143-353
 +
-identified good clones from ligations
-identified good clones from ligations
'''8/3/09'''
'''8/3/09'''
 +
-sent in ligations from 7/31/09 for sequencing
-sent in ligations from 7/31/09 for sequencing
 +
-set up fruiting bodies for ho46,180,181,182,193,201,203,227
-set up fruiting bodies for ho46,180,181,182,193,201,203,227
'''7/31/09'''
'''7/31/09'''
 +
-set up test digest for ligations
-set up test digest for ligations
 +
-ran a gel for tests digests
-ran a gel for tests digests
'''7/29/09'''
'''7/29/09'''
 +
-miniprepped plasmid amps and BPGW
-miniprepped plasmid amps and BPGW
 +
-xformed into dicty ho46: pho303,304,309,311,314,317,322
-xformed into dicty ho46: pho303,304,309,311,314,317,322
'''7/28/09'''
'''7/28/09'''
 +
-set up to take movies for ho46,159,164,171,178,179,193,201,203
-set up to take movies for ho46,159,164,171,178,179,193,201,203
 +
-set up cultures for ligations, bpgw and plasmid amp
-set up cultures for ligations, bpgw and plasmid amp
'''7/24/09'''
'''7/24/09'''
 +
-set up PCR for new part w/ ho388-ho389 primers on pho337
-set up PCR for new part w/ ho388-ho389 primers on pho337
 +
-set up ligations for PAKAN w/ all Cd's
-set up ligations for PAKAN w/ all Cd's
 +
-ran gel for PCR of pho337 w. ho388-389
-ran gel for PCR of pho337 w. ho388-389
 +
-set up GWBP for PCR product
-set up GWBP for PCR product
 +
-xformed ligations and BPGW and plasmid amps-pho 303,304,309,317,322
-xformed ligations and BPGW and plasmid amps-pho 303,304,309,317,322
'''7/23/09'''
'''7/23/09'''
 +
-recorded movies of ho46,159,164,171,178,179,193,203
-recorded movies of ho46,159,164,171,178,179,193,203
 +
-ran Aar1 digests on a gel of 1,6,7,8,60,50,66,97
-ran Aar1 digests on a gel of 1,6,7,8,60,50,66,97
 +
-gel purified fragments
-gel purified fragments
'''7/22/09'''
'''7/22/09'''
 +
-set up Aar1 digest for 1,6,7,8,60,66,50,97
-set up Aar1 digest for 1,6,7,8,60,66,50,97
'''7/21/09'''
'''7/21/09'''
 +
-miniprepped cultures for GWBP 1,6,7,8
-miniprepped cultures for GWBP 1,6,7,8
 +
-ran a gel for Aar1 digest of GWBP parts: 2,3,4,5
-ran a gel for Aar1 digest of GWBP parts: 2,3,4,5
 +
-gel purified fragments
-gel purified fragments
 +
-xformed pho 223, 228, 233, 341, 342, 343 into ho2
-xformed pho 223, 228, 233, 341, 342, 343 into ho2
 +
-sent in sequencing of minipreps od 1,6,7,8
-sent in sequencing of minipreps od 1,6,7,8
'''7/20/09'''
'''7/20/09'''
 +
-set up cultures of pho223,233,228 and PCRs of new parts 1,6,7,8
-set up cultures of pho223,233,228 and PCRs of new parts 1,6,7,8
 +
-set up aar1 digest of 2,3,4,5 pcrs (fkbp and frbs)
-set up aar1 digest of 2,3,4,5 pcrs (fkbp and frbs)
'''7/17/09'''
'''7/17/09'''
 +
-rna gel of pcrs to check new parts--success
-rna gel of pcrs to check new parts--success
 +
-xformed 32 of 71 plasmids into ho2 (Pi3k1/2 minus)
-xformed 32 of 71 plasmids into ho2 (Pi3k1/2 minus)
 +
-GWBP pcrs of pakan, pipkj, and pten
-GWBP pcrs of pakan, pipkj, and pten
 +
-froze ho201
-froze ho201
'''7/16/09'''
'''7/16/09'''
 +
-miniprepped cultures
-miniprepped cultures
 +
-sent sequencing for Pd, PD*, pipk-2, pho112
-sent sequencing for Pd, PD*, pipk-2, pho112
 +
-set up pcr for pakan and pipkj again
-set up pcr for pakan and pipkj again
 +
-set up fruiting body assay for ho171, 159, 46
-set up fruiting body assay for ho171, 159, 46
 +
-set up pcr for pakan, pipkj and new piece, pten (1-16 delta)
-set up pcr for pakan, pipkj and new piece, pten (1-16 delta)
 +
-ran gel for PCR--success
-ran gel for PCR--success
 +
-xformed pho223 and 233 again
-xformed pho223 and 233 again
 +
-set up culture for bp reactions of new parts
-set up culture for bp reactions of new parts
 +
-froze ho193
-froze ho193
'''7/15/09'''
'''7/15/09'''
 +
-set up pcr for new parts: PakaN, FKBP, FKBP, FKBP, FRB, INP54, PIPKJ
-set up pcr for new parts: PakaN, FKBP, FKBP, FKBP, FRB, INP54, PIPKJ
 +
-ran pcrs on gel to see if it worked--pakan and pipkj did not work
-ran pcrs on gel to see if it worked--pakan and pipkj did not work
 +
-set up pcrs for gwbp
-set up pcrs for gwbp
 +
-xformed into bacteria
-xformed into bacteria
 +
-set up cultures of plasmid amp
-set up cultures of plasmid amp
'''7/14/09'''
'''7/14/09'''
 +
-added hygromycin to xformations
-added hygromycin to xformations
 +
-checked sequences, alw150 is actually ~250bp, not ~1900.
-checked sequences, alw150 is actually ~250bp, not ~1900.
 +
-xformed plasmids for amplifications
-xformed plasmids for amplifications
'''7/13/09'''
'''7/13/09'''
 +
-xformed pho303,304,309,311, 317 into ho46
-xformed pho303,304,309,311, 317 into ho46
 +
-sent in alw150 from ben for sequencing
-sent in alw150 from ben for sequencing
'''7/10/09'''
'''7/10/09'''
 +
-ran gel for colony pcr--not enough template
-ran gel for colony pcr--not enough template
 +
-set up test digest of same samples of colony pcr
-set up test digest of same samples of colony pcr
 +
-ran gel for test digests--success
-ran gel for test digests--success
'''7/9/09'''
'''7/9/09'''
 +
-ran gel for Aar1 digests--success
-ran gel for Aar1 digests--success
 +
-gel purified frags
-gel purified frags
 +
-set up ligations for alw150 w/ pho50
-set up ligations for alw150 w/ pho50
 +
-set up colony pcr for alw150 w/ pho 93,92
-set up colony pcr for alw150 w/ pho 93,92
 +
-set up cultures for colony pcr samples
-set up cultures for colony pcr samples
 +
-xformed ligations  
-xformed ligations  
 +
-set up strains for fruiting bodies HO 178, 171, 159, 172, 46
-set up strains for fruiting bodies HO 178, 171, 159, 172, 46
'''7/8/09'''
'''7/8/09'''
 +
-miniprepped cultures
-miniprepped cultures
 +
-set up pvu1 digests
-set up pvu1 digests
 +
-set up Aar1 digests for ALW150 and pho50
-set up Aar1 digests for ALW150 and pho50
 +
-ran gel for test digests
-ran gel for test digests
 +
-pho92 frag is good, most worked.
-pho92 frag is good, most worked.
 +
-set up ligations of alw150 with pho92 and pho 93
-set up ligations of alw150 with pho92 and pho 93
 +
-sent in sequences
-sent in sequences
 +
-heat inactivated Aar1 digests
-heat inactivated Aar1 digests
 +
-xformed ligations  
-xformed ligations  
'''7/7/09'''
'''7/7/09'''
 +
-set up cultures of ligations
-set up cultures of ligations
 +
-Set up Aar1 digests of pho50,92,93,99
-Set up Aar1 digests of pho50,92,93,99
 +
'''7/6/09'''
'''7/6/09'''
 +
-xformed pho268, 267, 272 and 271 into ho46  
-xformed pho268, 267, 272 and 271 into ho46  
 +
-set up ligations of pho55, 66, 99, 132, 143, 144 into pho189
-set up ligations of pho55, 66, 99, 132, 143, 144 into pho189
 +
-set up GWLR for pho 255,264,259,256,262,260,263 into pho203
-set up GWLR for pho 255,264,259,256,262,260,263 into pho203
 +
-xformed ligations and gateways into dh5a
-xformed ligations and gateways into dh5a
'''7/2/09'''
'''7/2/09'''
 +
-miniprepped cultures for rassl
-miniprepped cultures for rassl
 +
-sent out rassl for sequencing
-sent out rassl for sequencing
 +
-created bc linkers with oligos
-created bc linkers with oligos
 +
-CIP'd Aar1 digest of pho189
-CIP'd Aar1 digest of pho189
 +
-created BC linker again
-created BC linker again
 +
-pcr purified Aar1 digest w/ cip
-pcr purified Aar1 digest w/ cip
 +
-ran pho189 digests on a gel --success
-ran pho189 digests on a gel --success
'''7/1/09'''
'''7/1/09'''
 +
-set up digest of pho97 and pho189 with nru1 and bamh1/xba1 respectively
-set up digest of pho97 and pho189 with nru1 and bamh1/xba1 respectively
 +
-pcr purified digests
-pcr purified digests
 +
-set up aar1 digest for both
-set up aar1 digest for both
 +
-set up cultures of RASSL in pDONR221 from GWBP
-set up cultures of RASSL in pDONR221 from GWBP
'''6/30/09'''
'''6/30/09'''
 +
-Set up cultures of GWLR reactions in destination vectors and cultures of storage vectors for Aar1
-Set up cultures of GWLR reactions in destination vectors and cultures of storage vectors for Aar1
'''6/29/09'''
'''6/29/09'''
 +
-CAR1 was good but RASSL was not
-CAR1 was good but RASSL was not
 +
-Set up PCR with new RASSL template
-Set up PCR with new RASSL template
 +
-Ran a Gel for PCR
-Ran a Gel for PCR
 +
-RASSL is good
-RASSL is good
'''6/16/09'''
'''6/16/09'''
 +
-Sent in RASSL and CAR1 in PDONR221 for sequencing
-Sent in RASSL and CAR1 in PDONR221 for sequencing
'''6/15/09'''
'''6/15/09'''
 +
-Set up cultures for RASSL and CAR1 in PDONR221
-Set up cultures for RASSL and CAR1 in PDONR221
'''6/11/09'''
'''6/11/09'''
 +
-Ran a gel for PCR's
-Ran a gel for PCR's
 +
-Gel purified both fragments
-Gel purified both fragments
 +
-Did a gateway BP reaction
-Did a gateway BP reaction
'''6/10/09'''
'''6/10/09'''
 +
-Set up PCR to amplify RASSL and CAR1
-Set up PCR to amplify RASSL and CAR1

Revision as of 23:58, 14 October 2009

10/9/09

-miniprepped cultures from 10.7.09 and sent in for sequencing

10/7/09

-set up cultures for 3

10/2/09

-checked sequences

9/30/09

-miniprepped cultures for 1,3,4,5,6,8

-sent in sample for sequencing

9/28/09

-ran gel for PCRs

-set up cultures for 1,3,4,5,6,8

9/25/09

-Set up PCR for biobrick parts 2 and 9 with elongase

9/18/09

-ran PCR again for 2 and 9 using KOD

-ran gel for PCR

9/11/09

-ran gel again for PCRs

9/9/09

-ran a gel for PCRs

-set up BPGW for PCRs

-xformed into dh5alpha

9/4/09

-set up PCR for biobricks

-DPN1 treated

-PCR purified

8/26/09

-set up test digest for ligations of 347-92,93 and FRB-FKBP-FKBP

-ran a gel for test digests

8/21/09

-made movies of ho46,320,331,332,333,334,335

8/19/09

-set up cultures for ligations of pho347-93,92 and FRB-FKBP-FKBP

8/13/09

-heat inactivated Aar1 digest

-ran gel for digest

-gel purified

-set up ligations for pho347 w/ 92,93 and AB FRB, BC FKBP, CD FKBP

8/12/09

-miniprepped pho347

-set up Aar1 digest of pho347 o/n

8/11/09

-miniprepped LR cultures

-sent in for sequencing (LRs)

-made movie of ho46,320,331,332,333,334

-set up culture for pho347

8/10/09

-froze ho335,336

-set up cultures for LRs of pho203-pho275 to pho203-pho382

-xformed pho347 for plasmid amp

8/7/09

-made movies of ho46,180,181,182,227

-checked sequences

8/6/09

-sent in samples for sequencing from 8/5/09 test digest

-set up LR rxn for pho375,376,377,378,379,380,381

8/5/09

-set up LRGW for good clones of ligations

-froze ho46 w/ pho304 --ho3

-miniprepped cltures from 8/4/09

-set up test digest for minipreps

-ran a gel for test digests

8/4/09

-set up for movies of ho46,179,180,181,182,227

-set up cultures for 347-50-60-92-93-143-353

-identified good clones from ligations

8/3/09

-sent in ligations from 7/31/09 for sequencing

-set up fruiting bodies for ho46,180,181,182,193,201,203,227

7/31/09

-set up test digest for ligations

-ran a gel for tests digests

7/29/09

-miniprepped plasmid amps and BPGW

-xformed into dicty ho46: pho303,304,309,311,314,317,322

7/28/09

-set up to take movies for ho46,159,164,171,178,179,193,201,203

-set up cultures for ligations, bpgw and plasmid amp

7/24/09

-set up PCR for new part w/ ho388-ho389 primers on pho337

-set up ligations for PAKAN w/ all Cd's

-ran gel for PCR of pho337 w. ho388-389

-set up GWBP for PCR product

-xformed ligations and BPGW and plasmid amps-pho 303,304,309,317,322

7/23/09

-recorded movies of ho46,159,164,171,178,179,193,203

-ran Aar1 digests on a gel of 1,6,7,8,60,50,66,97

-gel purified fragments

7/22/09

-set up Aar1 digest for 1,6,7,8,60,66,50,97

7/21/09

-miniprepped cultures for GWBP 1,6,7,8

-ran a gel for Aar1 digest of GWBP parts: 2,3,4,5

-gel purified fragments

-xformed pho 223, 228, 233, 341, 342, 343 into ho2

-sent in sequencing of minipreps od 1,6,7,8

7/20/09

-set up cultures of pho223,233,228 and PCRs of new parts 1,6,7,8

-set up aar1 digest of 2,3,4,5 pcrs (fkbp and frbs)

7/17/09

-rna gel of pcrs to check new parts--success

-xformed 32 of 71 plasmids into ho2 (Pi3k1/2 minus)

-GWBP pcrs of pakan, pipkj, and pten

-froze ho201

7/16/09

-miniprepped cultures

-sent sequencing for Pd, PD*, pipk-2, pho112

-set up pcr for pakan and pipkj again

-set up fruiting body assay for ho171, 159, 46

-set up pcr for pakan, pipkj and new piece, pten (1-16 delta)

-ran gel for PCR--success

-xformed pho223 and 233 again

-set up culture for bp reactions of new parts

-froze ho193

7/15/09

-set up pcr for new parts: PakaN, FKBP, FKBP, FKBP, FRB, INP54, PIPKJ

-ran pcrs on gel to see if it worked--pakan and pipkj did not work

-set up pcrs for gwbp

-xformed into bacteria

-set up cultures of plasmid amp

7/14/09

-added hygromycin to xformations

-checked sequences, alw150 is actually ~250bp, not ~1900.

-xformed plasmids for amplifications

7/13/09

-xformed pho303,304,309,311, 317 into ho46

-sent in alw150 from ben for sequencing

7/10/09

-ran gel for colony pcr--not enough template

-set up test digest of same samples of colony pcr

-ran gel for test digests--success

7/9/09

-ran gel for Aar1 digests--success

-gel purified frags

-set up ligations for alw150 w/ pho50

-set up colony pcr for alw150 w/ pho 93,92

-set up cultures for colony pcr samples

-xformed ligations

-set up strains for fruiting bodies HO 178, 171, 159, 172, 46

7/8/09

-miniprepped cultures

-set up pvu1 digests

-set up Aar1 digests for ALW150 and pho50

-ran gel for test digests

-pho92 frag is good, most worked.

-set up ligations of alw150 with pho92 and pho 93

-sent in sequences

-heat inactivated Aar1 digests

-xformed ligations

7/7/09

-set up cultures of ligations

-Set up Aar1 digests of pho50,92,93,99


7/6/09

-xformed pho268, 267, 272 and 271 into ho46

-set up ligations of pho55, 66, 99, 132, 143, 144 into pho189

-set up GWLR for pho 255,264,259,256,262,260,263 into pho203

-xformed ligations and gateways into dh5a

7/2/09

-miniprepped cultures for rassl

-sent out rassl for sequencing

-created bc linkers with oligos

-CIP'd Aar1 digest of pho189

-created BC linker again

-pcr purified Aar1 digest w/ cip

-ran pho189 digests on a gel --success

7/1/09

-set up digest of pho97 and pho189 with nru1 and bamh1/xba1 respectively

-pcr purified digests

-set up aar1 digest for both

-set up cultures of RASSL in pDONR221 from GWBP

6/30/09

-Set up cultures of GWLR reactions in destination vectors and cultures of storage vectors for Aar1

6/29/09

-CAR1 was good but RASSL was not

-Set up PCR with new RASSL template

-Ran a Gel for PCR

-RASSL is good

6/16/09

-Sent in RASSL and CAR1 in PDONR221 for sequencing

6/15/09

-Set up cultures for RASSL and CAR1 in PDONR221

6/11/09

-Ran a gel for PCR's

-Gel purified both fragments

-Did a gateway BP reaction

6/10/09

-Set up PCR to amplify RASSL and CAR1

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