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 DateSummary
9/4Miniprepped and sent 2 copies of B9t9 for sequencing
9/15
  • LRs (all in pDEST 4-5)
    • hEF1a:Gal4VP16
    • CuO:VRC01 Heavy
    • CuO:VRC01 Light
    • CuO:HyHEL10 Light
    • CuO:HyHEL10 Heavy
9/16

CuO:VRCO1 Heavy, hEF1a:Gal4VP16, and pENTR Gal4VP16 transformed and plated.

CuO: VRCO1 Light, Cuo:HyHEL10 Light and "" Heavy all failed so the failed three were replated using the remainder of the transformation outgrowth culture.

9/17 
9/19

TC:

  • HEK293 ft cells (P8) frozen down (at 10^6/mL) - currently in -140C in room 115, back left corner, 1st box in column labelled iGEM cells
  • hEF1a-CuO:VRC01 heavy mini culture in fridge
9/20
  • Miniprepped :
    • hEF1a-CuO:VRC01 L
    • hEF1a-CuO:HyHEL10 L
    • hEF1a-CuO:HyHEL10 H
9/22
  • Digest and Gel
    • CuO:VRCOI L
    • CuO:VRCOI H
    • CuO:HyHEL 10 L
    • CuO:HyHEL 10 H
    • All Syk - X - TEV Midis
    • All Syk - X - tTEV Midis
    • hEF1a: Gal4VP16
10/7
  • Digest
    • CuO:VRC01 L
    • CuO:HyHEL10 L
    • CuO:HyHEL10 H
10/8
  • Gel
    • CuO:VRC01 L
    • CuO:HyHEL10 L
    • CuO:HyHEL10 H
  • Digest/gel
    • pENTR hEF1a-CuO
10/18BP and LR Digests
10/20BP and LR Gels
10/26
  • LRs (using #1 of pENTRs and pDEST 4-5)
    • CuO:A12T12
    • CuO:A12T6
    • CuO:A9T15
11/3
  • Transform LRs
    • CuO:A12T12
    • CuO:A12T6
    • CuO:A9T15
11/4
  • Pick colonies
    • CuO:A12T12
    • CuO:A12T6
    • CuO:A9T15
11/5
  • Digest
    • CuO:A12T12
    • CuO:A12T6
    • CuO:A9T15
  • Redigest
    • CuO:Gmab H
    • CuO:Gmab L
    • CuO:CD79A
    • CuO:CD79B
    • CuO:Lyn
  • Start midipreps
    • CuO:Gmab H
    • CuO:Gmab L
    • CuO:CD79A
    • CuO:CD79B
    • CuO:Lyn
11/7
  • Redigest
    • CuO:A12T12
    • CuO:A12T6
    • CuO:A9T15
  • Split cells (P5) - there are three plates (the cells looked really clumpy so I tried different ways of unclumping them, it's possibly because the pipetter wouldn't release properly)
  • Spin down and freeze midiprep cultures
11/15
  • midi: cuo:gmabh, gmabl, cd79a, cd79b, lyn, cd79a-9t15
  • mini cuo:cd79a-12t6, cd79a-12t12 more colonies
  • (digest: apa)

 

 

 

 

 

 

 

 

 

 

LRs (using #1 of pENTRs and pDEST 4-5)
  • CuO:A12T12
  • CuO:A12T6
  • CuO:A9T15
Expand
titleSpring
DateSummary
03/23Verification of linker-switchable PCRs
04/01
  • rePCRs of CD79B, Gal4 and RFP to make linker switchable constructs
  • Gel verification of 03/31 and 04/01 PCRs
04/10
  • rePCRs of CD79A/B, Gal4 and RFP to make linker switchable constructs
  • Gel verification of PCRs
04/11redesign CD79A/B primers
04/25
  • rePCRs of CD79A/B, to make linker switchable constructs
  • Gel verification of PCRs
04/30
  • rePCR of CD79B with DMSO
  • gel purification of CD79A
  • PCR purification of pTet:mRFP and Gal4VP16
  • AarI golden gate to make hEF1a:CD79A-pTet:mRFP-Gal4VP16
05/01
05/04
05/06
05/29
  • Transformations for Glycerol Stocks
  • Sent for hEF1a:CD79B-TCS-Gal4VP16 sequencing
  • PCRd CD79B
  • CD79B Gel
05/30
  • CD79B Gel Extraction (Failed)
  • Midi Cultures Inocculated
  • CD79B PCR 2
  • Picked Colonies for H:Lyn, H:LT, H:CB-TCS-G4
05/31
  • CD79B PCR Gel
  • CD79B Gel Extraction
  • hEF1a:CD79B-pTet:RFP-Gal4VP16 Golden Gate
  • h:Lyn-TEV colonies picked
Expand
titleJune
DateSummary
06/01
  •  h:Lyn-TEV Colonies Picked
  • h:CDB-RFP-G4 transformation
  • h:CDA-RFP-G4 Sequence Analysis
  • Inocculate Midipreps
  • h:Lyn, h:CDB-TCS-G4 cryostocks
06/02
  • Cloning Redesign
  • Pick hEF1a:CD79B-pTet:RFP-Gal4VP16 Colonies
06/03
  • Miniprep hEF1a:CD79B-pTet:RFP-Gal4VP16
  • Cryostock hEF1a:CD79A-pTet:RFP-Gal4VP16
06/04
  • Glycerol Stock hEF1a:CD79A-pTet:RFP-Gal4VP16
  • Midiprep 4 Frozen pellets
  • Digest & Gel hEF1a:CD79B-pTet:RFP-Gal4VP16
06/08
  • hEF1a:CD79B-pTet:RFP-Gal4VP16 Digest & gel
06/09
  • Send for sequencing
06/11
  • Sequencing Analysis
  • Glycerol Stock H:CDA-RFP-G4
06/16
  • designed SDM primers
  • LR TRE:mKate, hEF1a:LacI, pLac:mKate
  • experimental design + deadlines
06/17
  • annealed linker halves
  • CD79A linker golden gates
06/18
  • transformed CD79A linker golden gates
  • transformed LRs (TRE:mKate, pLac:mKate, hEF1a:LacI)
  • LRed TREt:VP16Gal4
06/19
  • sdm primers are here
  • killed LR TREt:VP16Gal4
  • Transformed LR TREt:VP16Gal4
  • Re-transformed CA-9T6-G4
  • picked CD79A linker colonies
06/21
  • picked CA-9T6-G4 colonies
06/22
  • mini CD79A linkers
  • mini TRE:mKate, pLac:mKate, hEF1a:LacI
  • digest
  • run CD79B SDM gel
06/23
  • digests and gels for TRE:mKate, pLac:mKate, hEF1a:LacI
  • kill TRE:Gal4VP16 LR
  • transform TRE:Gal4VP16 LR
  • run SDM on gel -> gel extraction
  • CD79B-RFP-G4 SDM product transformation
06/24
  • SDM CD79B-RFP-Gal4
  • SDM DpnI digest
  • transform SDM product
  • transform TRE:Gal4VP16
06/25
  • redigest TRE:mKate, pLac:mKate, hEF1a:LacI
  • PCR syk, tevp, ttevp
  • gel verify PCRs and digested LRs
  • TRE:gal4VP16 pick colonies and minipreps
  • PCR purification of syk, tevp, ttevp
  • reLR of TRE:mKate, pLac:mKate, hEF1a:LacI
  • retransform SDM digests
06/26
  • TRE:gal4vp16 gel
  • TRE:syk-mrfp-tevp golden gates
06/28
  • transform golden gates
06/29
  • cultured and miniprepped LR2 TRE:mKate, pLac:mKate, hEF1a:LacI
  • miniprepped LR1 TRE:mKate, pLac:mKate, hEF1a:LacI
  • digest and gel LR1 TRE:mKate, pLac:mKate, hEF1a:LacI
  • picked colonies of new TRE:gal4vp16 transformation

06/30
Expand
titleJuly
DateSummary
07/01

07/02 

Cumate Switch:

  • Kill LR
  • Transform LR product

Lac Switch:

SDM:

MIDIs:

  • TRE:Gal4VP16
  • TRE:mKate
  • hEF1a:LacI

Mini Cultures:

  • pENTR hEF2a-LacO
  • pENTR LacI
07/03
  • Verification digests of all midis + redigests of CD79A linker golden gates
  • midi pLac:mKate
  • mini pENTR hEF1a-LacO and pENTR LacI + digest
  • pick pENTR mKate + mini

SDM plates didn't grow any colonies

07/05
  • Transform TRE:Syk-pTet:RFP-TEV, TRE:Syk-pTet:RFP-tTEV, hEF1a:CD79A-pTet:RFP-gal4VP16 SDM, hEF1a:CD79B-pTet:RFP-Gal4VP16 SDM
  • Plate remainder of failed SDMs
07/06
  • digest, gel:
    • pENTR mKate
    • hEF1a:Gal4VP16 
    • pENTR CD79B-TCS-Gal4VP16
  • sequence:
  • transform:
    • TRE:syk
    • Re-transform CD79A-TCS-G4 and CD79B-TCS-G4 SDM Golden Gates
  • pick colonies:
    • CD79A-3TCSX-Gal4VP16 colonies
    • CD79A SDM colonies
    • hEF1a:CymR, hEF1a-CuO:mKate, CMV5-CuO:mKate
07/07
07/08
07/09
  • gel:
  • TRE:Syk-15-tTEVp PCR purification
  • TRE:Syk-15-tTEVp golden gate
  • LRs:
    • EGSH:mKate
    • hEf1a:VgEcR-2A-RXR
    • hEF1a:Gal4VP16
    • TRE:mKate
    • hEF1a:CD79B-TCS-Gal4VP16 
    • hEF1a:tagBFP
  • Midi Cultures
07/10
  • Repeat sequencing of CD79A Gal4 SDM #1 since the gal4 read (#4) showed correct mutaiton
  • midi cultures
  • Transformations:
    • RE:Syk-15-tTEVp golden gate
    • Golden gate donor
    • LRs:
      • EGSH:mKate
      • hEf1a:VgEcR-2A-RXR
      • TRE:mKate
      • hEF1a:Gal4VP16 (remember which pDEST)
      • hEF1a:CD79B-TCS-Gal4VP16 
      • hEF1a:tagBFP
07/11

 

07/12

 

07/13
  • Reinnoculate midis:
  • Pick colonies:
    • EGSH:mKate
    • hEf1a:VgEcR-2A-RXR
    • TRE:mKate
    • hEF1a:Gal4VP16 (remember which pDEST)
    • hEF1a:CD79B-TCS-Gal4VP16 
    • hEF1a:tagBFP
07/14
07/15
  • IgM constant region + RFP PCRs +gel
  • IgM-RFP golden gate
  • Transform CD79A linker golden gates and remainder of LRs for cultures that didn't grow today:
    • TRE:Syk-15-tTEVp
    • TRE:mKate
    • EGSH:mKate
    • hEF1a:VgEcR-2A-RxR
    • hEF1a:Gal4VP16
    • hEF1a:CD79B-TCS-Gal4VP16
  • Ordered Primers:
07/16
  • innoculate:
    • TRE:Syk-15-tTEVp
    • TRE:mKate
    • EGSH:mKate
    • hEF1a:VgEcR-2A-RxR
    • hEF1a:Gal4VP16
    • hEF1a:CD79B-TCS-Gal4VP16
    • CD79A-3T3-Gal4
    • CD79A-6T6-G4
    • CD79A-6T12-G4
    • CD79A-9T3-G4
  • replate CD79A linker golden gate transformations that didn't give colonies
07/17
  • replated golden gates didn't give any colonies (may have used too little DNA)
  • miniprep, digest, gel:
    • TRE:Syk-15-tTEVp
    • TRE:mKate
    • EGSH:mKate
    • hEF1a:VgEcR-2A-RxR
    • hEF1a:Gal4VP16
    • hEF1a:CD79B-TCS-Gal4VP16
    • CD79A-3T3-Gal4
    • CD79A-6T6-G4
    • CD79A-6T12-G4
    • CD79A-9T3-G4
  • CD79A linker golden gates
  • innoculate midis
07/18
  • CD79A linker golden gate T4 ligation
  • Transform CD79A golden gates
  • Midipreps:
    • hEF1a:Gal4
    • hEF1a:tagBFP
    • hEF1a:VgEcR-2A-RxR
    • EGSH:mKate
    • hEF1a:CD79B-TCS-Gal4VP16
    • TRE:mKate
07/19
  • CD79A linker golden gates liquid cultures
07/20
  • Miniprep CD79A golden gate liquid cultures
  • Digest, gel:
    • CD79A linker
    • hEF1a:Gal4
    • hEF1a:tagBFP
    • hEF1a:VgEcR-2A-RxR
    • EGSH:mKate
    • hEF1a:CD79B-TCS-Gal4VP16
    • TRE:mKate
  • IgM-RFP pENTR golden gate transformation
07/21
  • CD79B & Gal4VP16 PCRs
  • Gel to test Oligo Annealing
  • Anneal Oligos in annealing buffer
  • Golden Gates
  • Transform
  • Pick pENTR RFP-IgM Colony
  • Sequencing:
07/22
07/23
07/24
  • gel cd79a-linker-gal4vp16:
    • 3t3
    • 3t15
    • 6t9
    • 9t15
    • 12t9
    • 12t12
  • send for sequencing
    • 3t3
    • 6t9
    • 9t15
    • 12t9
    • 12t12
  • midis
    • 3t9
    • 6t6
    • 6t12
    • 9t3
    • 9t6
    • 12t6
  • mini digests gels
  • rePCR RFP
  • Golden gates
  • Transformations
  • mini, digest, gel
    • 6T9
    • 9T12
    • 9T15
    • 12T9
    • 12T12
  • send for sequencing:
    • 3T15
    • 15T9
07/25 
07/26 
07/27
  • AarI verification gel
  • CD79A linker midis
  • innoculate CD79A linker midis
  • innoculate Syk-linker minis
  • innoculate CD79A failed linker minis
  • Golden gates:
    • VRC01 heavy + light pENTR
    • HyHel10 heavy + light pENTR
07/28
  • Mini, digest, gel:
    • TRE:Syk-3-tTEVp
    • TRE:Syk-6-tTEVp
    • TRE:Syk-9-tTEVp
    • TRE:Syk-12-tTEVp
    • hEF1a:CD79A-9T15-G4
  • Midi, digest, gel:
    • CD79A-6T9-G4
    • CD79A-9T9-G4
    • CD79A-9T12-G4
    • CD79A-15T3-G4
    • CD79A-15T15-G4
    • hEF1a:Gal4
  • Sequencing:
    • resend 12T12
    • 9T15
  • Transform Golden gates:
    • VRC01 heavy + light pENTR
    • HyHel10 heavy + light pENTR
    • Syk-15-tTEVp retransformation
    • CD79B-RFP-G4 retransformation
07/29
  • Mini, digest gel:
    • CD79A-3T15-G4
    • CD79A-12T9-G4
    • CD79A-15T9-G4
  • Golden Gates
  • Sequencing
07/30
  • mini, digest, gel
  • midi, digest, gel
    • A-3T3
    • GG Donr
  • Innoculate Mini cultures with successful GGs
  • Innoculate midi culture
  • Replated failed GG transformations
    • TRE:Syk-6-tTEVp
    • TRE:Syk-9-tTEVp
  • sequencing:
    • 3T15 - okay -> resequencing
    • 15T9 - bad
    • VRC01 H pENTR - good
    • VRC01 L pENTR - bad quality -> resequencing
    • HyHEL10 H pENTR - bad quality -> resequencing
07/31
  • mini, digest, gel
    • CD79A-12T12-G4
    • Syk-15-tTEVp pENTR
    • HyHel10 Light pENTR
  • Midi, digest, gel
    • A-12T9
  • Innoculate minis
    • TRE:Syk-12-tTEVp
    • TRE:Syk-3-tTEVp
    • hEF1a:CD79B-pTET:mRFP-G4
    • A-15T9
    • A-12T12
    • A-9T15
    • A-3T15
  • Sequencing
    • A-12T12
    • HyHEL 10 L pENTR
    • Syk-15-tTEVp pENTR
Expand
titleAugust
 DateSummary
08/03
  • miniprep, digest, gel:
    • CD79B-RFP-G4 1,2,3
    • TRE:Syk-3-tTEVp
    • CD79A-3T15-G4 1,2
    • CD79A-9T15-G4 1,2
    • CD79A-15T9-G4 1,2
    • Midi redigests:
      • A3T3
      • A12T9
  • Sequencing
    • A3T15 #1
    • A9t15 #2
    • A15T9 #1
    • CD79B-RFP-G4 #1
    • TRE:Syk-3-tTEVp
08/04
  • Midi, digest, gel
    • A-12T12 (good gel - bad yield -> regrew more to midi on 08/05
  • Miniprep, digest, gel
    • TRE:Syk-6-tTEVp 1,2
  • Sequencing
    • VRC01L
    • TRE:Syk-6-tTEVp #1
  • Kill, transform
    • TRE:Syk-15-tTEVp LR
  • Innoculate:
    • A-12T12 midi
    • T:S-3-tT
    • T:S-6-tT
    • T:S-9-tT
    • T:S-12-tT
08/05
  • Miniprep:
    • T:S-9-tT 1,2
    • T:S-12-tT 1,2
  • Midi:
    • A-12T12
  • Sequence:
    • T:S-9-tT #1
    • T:S-12-tT #1
    • A-3T15 #2
    • A-9T15 #1
  • Pick:
  • Innoculate:
08/06 
08/07
  • LR TRE:Syk-15-tTEVp (pDEST 2-3)
  • Miniprep, send for sequencing:
    • B-3T3
    • B-3T9
    • B-6T6
    • B-6T9
    • B-9T3
    • B-9T6
    • B-9T12
    • B-12T6
    • B-12T9
    • B-12T12
    • B-15T3
    • B-15T15
  • Miniprep, digest, gel
    • TRE:Syk-15-tTEVp
  • Midiprep, digest, gel
    • TRE:Syk-6-tTEVp
  • Golden Gate
    • hEF1a:CD79A-15T9-G4 (because even though we midi'ed it, sequencing was bad)
    • TRE:Syk-linker-TEVp (3, 6, 9, 12)
    • hEF1a:CD79B-3T15-G4
    • hEF1a:CD79B-9T9-G4
  • Pick colonies
    • pENTR HyHEL10 Heavy
    • hEF1a:CD79B-9T15-G4
  • Restreak
    • hEF1a:CD79B-6T12-G4
    • hEF1a:CD79B-15T9-G4 (restreak and replate)
08/08
  • kill LR
  • Transform:
    • LR TRE:Syk-15-tTEVp
    • A-15T9
    • B-3T15
    • B-9T9
    • TRE:Syk-X-TEVp (X=3,6,9,12)
  • Restreak:
    • A-3T15
    • B-15T15
    • B-15T9
    • B-6T12
08/09
  • Restreak/replate:
    • B9T9
    • B15T15
  • Inoculate midis:
    • B3T3
    • B3T9
    • B6T6
    • B9T3
    • B9T6
    • B12T6
  • inoculate minis:
    • TRE:Syk-15-tTEVp -gg
    • TRE:Syk-3-TEVp -gg
    • TRE:Syk-6-TEVp -gg
    • TRE:Syk-9-TEVp -gg
    • TRE:Syk-12-TEVp -gg
    • A15T9 -gg
    • A3T15
    • A9T15
    • B3T15 -gg
08/10
  • Minis:
    • A-3T15
    • A-9T15
    • A-15T9 (only one tube)
    • TRE:Syk-3-TEVp
    • TRE:Syk-6-TEVp
    • TRE:Syk-9-TEVp
    • TRE:Syk-12-TEVp
    • B-3T15
    • B-6T12
    • B-9T15
    • TRE:Syk-15-tTEVp --> digest
    • pENTR HyHEL10 H
  • Midis:
    • B3T3
    • B3T9
    • B6T6
    • B9T3
    • B9T6
    • B12T6
  • Golden gate, transform:
    • A3T15
    • A9T15
  • Sequencing:
    • A-3T15 1
    • A-9T15 1
    • A-15T9
    • TRE:Syk-3-TEVp 1
    • TRE:Syk-6-TEVp 1
    • TRE:Syk-9-TEVp 1
    • TRE:Syk-12-TEVp 1
    • B-3T15 1
    • B-6T12 1
    • B-9T15 1
    • TRE:Syk-9-tT 2
    • TRE: Syk-12-tT 2
08/11
  • Run gel of TRE:syk-15-tTEVp: correct, inoculate midi
  • digest pENTR HyHEL10 H
  • Sequencing:
    • B6T9-1
    • B9T12-1
  • Inoculate midi:
    • B15T3
    • T:S-15-tT
  • Inoculate mini:
    • B9T9 - from plate
    • A3T15 - from plate
  • Restreak/replate:
    • B15T9
    • A9T15 - one white
    • B15T15
    • B9T9 - only one white
08/12
  •  Run gel for pENTR HyHEL10 H digest  
  • Transform:
    • B15T15
  • Mini, sequence:
    • A9T15
    • B9T9
  • Midi:
    • TRE:syk-15-tTp
  • inoculate midi:
    • B15T3
    • T:S-9-TEVp
    • T:S-12-TEVp
    • B9T12
  • inoculate mini:
    • A9T15
    • B15T9
    • B6T9
  • Sequencing
    • B6T12-2
    • pENTR HyHEL10H-1
    • A15T9-2
    • B9T9 (from 8/12)
  • Repeat sequencing:
    • T:S-3-T 1
    • T:S-6-T 1
    • T:S-9-tT 2
    • T:S-12-tT 2
    • B3T15 1
    • B9T15 1
    • B12T12 2

08/13

 
  • Midis:
    • B9T12
    • B15T3
    • S9TEV
    • S12TEV
  • Minis, sequencing 
    • B6T9
    • A9T15
  • Inoculate mini
    • B15T9
    • B15T15
    • B12T9
    • T:S-9-tT
    • T:S-12-tT
  • Inoculate midi:
    • B12T12-2
  • Sequencing:
    • B6T9-1
    • A9T15-2
    • A3T15-2
    • T:S-3-T 1
    • T:S-6-T-1
08/14
  • Midis
    • B12T12-2
  • Minis, sequencing
    • T:S-9-tT
    • T:S-12-tT
  • Order antibodies/antigens
  • Finish Gaussian Distribution gating code
  • Split Cells
  • Inoculate mini
    • B15T15
    • B6T12
    • B6T9
    • A3T15
  • Hef1a:GAL4? 
  • Retransform 
    • B9T9
    • A15T9
    • T:S-6-T
    • B15T9
    • B12T9
  • Sequencing, take 1
    • B9T15-2
    • B3T15-1
    • T:S9tT 1
    • T:S12tT 1
  • Sequencing, take 2
    • T:S3T #2
    • A9T15 #1 (8/12)
08/15
  • Miniprep/sequence
    • B15T15 - one red, one with no growth :/
    • B6T12
    • B6T9
    • A3T15
  • Inoculate minis
    • B9T9
    • A15T9
    • T:S-3-T
    • T:S-6-T
    • B12T9
    • B15T15
  • Analyze sequencing and go from there
08/16
  • Make amp plates
  • Replate
    • B12T9
    • B15T9
  • Inoculate miniprep cultures
    • A15T9
    • T:S-6-T
    • B9T9
  • Inoculate midiprep culture
    • A9T15
    • B6T9 probably B6T12
    • B6T12 probably B6T9
  • Miniprep and sequence
    • T:S-3-T
    • B15T15
  • Spin down and store midiprep cultures
    • T:S-9-tT
    • T:S-12-tT
  • Analyze sequencing data
    • B6T12
    • B6T9
    • A3T15
08/17
  • Send for sequencing

    • A3T15 #2 (8/15)
    • B3T15 #1
    • B9T15 #1 
  • Replate
    • B12T9
    • B15T9
  • Inoculate miniprep cultures
    • A15T9
    • T:S-6-T
    • B9T9
  • Inoculate midiprep culture
    • T:S-3-TEV
  • Spin down and store midiprep cultures
08/18
  • Golden gate, transform
    • A15T9
    • B3T15
    • B9T9
    • B9T15
    • B12T9
    • B15T9
  • Transform
    • lab stock of Gal4VP16
  • Miniprep, sequence
    • T:S-6-T
  • Inoculate miniprep
    • A3T15
    • A15T9
  • Spin down midiprep
    • T:S-3-TEV
08/19 
08/20