Team:Osaka/Notebook

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Calendar

July
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August
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week6 29 30 31
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week7 5 6 7 8 9 10 11
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week10 26 27 28 29 30
October
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Notebook

September 26 (Sun)

  1. Transfer to culture solution (yesterday's transformations)
  2. Miniprep of 1-6N, 2-2F, 1-6I, 021 faint hint of red detected
  3. Restriction digest
    • 1-6N, 1-6I with EcoRI, SpeI
    • 2-2F, 021 with XbaI, PstI
  4. Gel electrophoresis
    • (RESULTS?)
  5. Miniprep of parts moved to solution culture this morning
  6. Cut check with XbaI, PstI <- ??these are not biobrick plasmids!
    • Cel8 - ok
    • Cel44 - ??
    • Man26 - ok
    • Xyn10 - ??
  7. Ligations of 9/23 restriction digests (ADH1, ADH2, CYC1, ENO2, SUC2, glr) to 1-1C plasmid backbone digested at E, S sites
    • 026 - ADH1 terminator
    • 027 - ADH2 promoter
    • 028 - CYC1 terminator
    • 029 - ENO2 promoter
    • 030 - SUC2 leader sequence
    • 031 - glr (glutamate racemase)
  8. Transformation of ligation products
  9. Transfer of yesterday's transformations to solution culture: 001-2, 025

September 27 (Mon)

  1. PCR of Man26, CelB
  2. PCR of Man48 (??), CBM from XynAcc
  3. Restriction digests
    • 1-2M with EcoRI, SpeI for assembly later
    • Cel8, Cel44, Cel5 with EcoRI; Xyn10 with PstI (for checking?)
    • 001-2 with EcoRI, SpeI
    • 025 with XbaI, PstI
  4. Gel electrophoresis
  5. Ligations
    • 032: 1-2M as upstream, 019 as downstream, 1-3A as vector
    • 033: 1-2M as upstream, 020 as downstream, 1-3A as vector
    • 004: 001-2 as upstream, 1-2J as downstream, 1-3A as vector (remake using 001-2)
    • 005: 001-2 as upstream, 2-22P as downstream, 1-3A as vector (" ")
  6. Transformation of ligation products
  7. Transfer to solution culture: 026, 027, 028, 029, 030, 031

September 28 (Tue)

  1. Miniprep of 026, 027, 028, 030, 031
  2. Restriction digest
    • 026, 028, 031 with XbaI, PstI
    • 027, 030 with EcoRI, SpeI
  3. Gel electrophoresis
    • (RESULTS?)
  4. Ligation: repeat assemblies of 004, 005, 032, 033 yesterday
  5. Transformation of ligation products as well as 3-2P
IDPart NameResistanceDescription
3-2P<bbpart>BBa_</bbpart>A??

September 29 (Wed)

  1. Transfer to solution culture 025, 026, 027, 028, 030, 031
  2. Ligations (repeat of 9/26 with different dilution of 1-1C)
    • 026 - ADH1 terminator
    • 027 - ADH2 promoter
    • 028 - CYC1 terminator
    • 029 - ENO2 promoter
    • 030 - SUC2 leader sequence
    • 031 - glr (glutamate racemase)
  3. Transformation of 025, 026, 027, 028, 030, 031 (repeat just in case; previous plates almost all red colonies; cannot pick up colony with correct insert?)
  1. PCR
    • pgsB - cloning from plasmid
    • pgsB - amplification from 021
    • Man28 - amplification from previous product
  2. PCR purification of products
  1. PCR of CelB, XynA-CBM
  1. Miniprep of cultures inoculated this morning (total culture time: 12hr)
    • 025 -> ok (colorless)
    • 027 -> turned red; discarded
    • others: ok?
  2. Restriction digest of 026, 028, 031 with XbaI, PstI
  3. Transfer to solution culture (9/28 transformations of 004, 005, 032, 033, 3-2P)
  4. Gel electrophoresis of PCR products
  1. Restriction digests:
    • pgsB, Man (??) with EcoRI, SpeI
    • today's miniprepped plasmids with EcoRI
    • 1-1C with EcoRI, SpeI

September 30 (Thu)

  1. PCR cloning
    • CM10
    • CelB (repeat)
    • ADH1 terminator, CYC1 terminator, SUC2 leader sequence from yeast genome (repeat)
    • glr (repeat)
  2. PCR purification: CM10, XynA-CBM
  3. Restriction digest of all above PCR products with EcoRI, SpeI
  4. Gel electrophoresis
  1. Ligation of PCR products to 1-1C backbone
    • 021: pgsB
    • 025: XynA-CBM
    • 026: ADH1 terminator
    • 028: CYC1 terminator
    • 031: glr
    • 034: Man
    • 035: CM10
  2. Transformation of ligation products
  1. PCR cloning of CelB, SUC2, ECO2, ADH2 from genomic DNA
  2. Gel electrophoresis
    • (RESULTS?)
  1. Miniprep of 004, 005, 032, 033, 3-2P (9/29 solution culture)
  2. Restriction digest of miniprepped parts
    • 004, 005, 032 with EcoRI, SpeI (same as earlier today)
    • 033, 3-2P (same as on 9/29)
  3. Gel electrophoresis
    • (RESULTS?)

TO CHECK/CONFIRM

  • 'K1' (mentioned on 9/250 -> where did it come from?
  • 9/25 - miniprepped parts (inoculated 9/24) were plasmids from karita sensei? biobrick parts pcr-cloned on 9/23? why where these parts transformed immediately after miniprep?
  • 'CelB, Cel44A' etc vs 'Cel5, Cel8, Cel44' which nomenclature refers to what (received plasmids, pcr product?)

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