Toronto/Lab Notebook

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(Difference between revisions)
(→Oct. 12th, 2007)
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** Plasmid length: 2079 bp
** Plasmid length: 2079 bp
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* Enzyme activity:-
+
* Enzyme activity
** Recipe used:
** Recipe used:
*** Enzyme: 0.25 uL
*** Enzyme: 0.25 uL

Revision as of 02:17, 13 October 2007

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PartsCatalogue

Contents

Oct. 12th, 2007

Yusuf, Faareha, Talal

  • Transformation of N2 (New) into (AMP + KAN) plate.
    • It's in incubator.
  • MP of Q04400 (A,B)and I13033.
  • Length check for Q04400 (A,B).
  • Length check for R0082 (A,B)
    • Part length: 108 bp
    • Plasmid length: 2079 bp
  • Enzyme activity
    • Recipe used:
      • Enzyme: 0.25 uL
      • Plasmid (J04500): 1 uL
      • BSA: 0.5 uL
      • Buffer: 0.5 uL
      • Distilled water: 3.75 uL

Oct. 10th, 2007

Yusuf

  • Transformation of Q04400 in DH5a from DNA of 2006
    • Its in the incubator and needs to be MP o/n tomorrow
  • Quantitation of N1 and S01003 using previously digested parts
    • Whoever comes in tomorrow plz check if the parts match up. everything is in the notebook and also do the calculation to find out the concentration of both constructs if they match up to what is expected
  • Length check of the following:
    • E1B # 1 (A,B)
    • E1B # 2 (A,B)
    • R0082 (A,B)
    • I13504 (A,B)
      • For all these length checks enzyme combination Xba/Pst was used
  • Length Check:
  • Part Name Part Plasmid
  • E1B#1 A O O
  • E1B#1 B O O
  • E1B#2 A O O
  • E1B#2 B O O
  • I13504 A O O
  • I13504 B x x
  • R0082 A x O
  • R0082 B x O
  • Mp o/n of J06801
  • I13033: plate couldnt be found
  • Made:
    • 3 AMP+KAN
    • 3 KAN

TO DO:

  • MP o/n of Q04400
  • Ligation of N1 + S01003 using previously digested parts
    • Quantitation has already been done and the tubes for these are in the iGem 2007 box
  • Proceed with ligating OmpR promoter with GFP: R0082 + E0240. (Use I13504 if you think it's necessary)
  • Test S/P/E/X enzymes (all of them) to determine relative activity and record the order. Use one of the not commonly used plasmids
  • MP of J06801 A&B
  • Ligate if N1 and S01003 is correct

Oct. 9, 2007

  • Digest, GE, purify, quantitate:
    • I13033 A, S/P - Bands at: ~3500, ~3000 (cut out), 2000-1500
      • [I13033] = 0 ng/uL
    • J06801 A, E/X - Bands at: ~6000 (cut out)
      • [J06801] = 0 ng/uL
    • Q04400 C, X/P - Bands at: none
  • Mini-prep E1b #1 AB, E1b #2 AB (#1 and #2 denote plate numbers)
  • length check (O = match, X = non-match):
Part NamePartPlasmid
N2 AXO
N2 BXO
N2 CXO
N2 DXO
  • For N2, the part length corresponded to ~1000 bp, which is the length of both N1 and S01003.
  • Hold off on length checking R0062 (may or may not happen)

To Do:

  • Length check of E1b #1 AB, E1b #2 AB
  • Make plates when you need them. (We have 2 large agar flasks, and if you do melt one, maybe split it into 2 flasks)
  • Proceed with ligating OmpR promoter with GFP: R0082 + E0240. (Use I13504 if you think it's necessary)
  • Test S/P/E/X enzymes (all of them) to determine relative activity and record the order. Use one of the not commonly used plasmids
  • Re-ligate N1 + S01003 using previously digested parts (make sure to quantitate again)
  • Transform Q04400 into DH5a
  • Make o/n of J06801 A, I13033 A (4 x 2.5 mL each) - this is to address the low DNA concentrations; we will combine them into 2 super MPs (the MP kit can only handle a max of 5 mL of o/n per tube). We will then combine them in the gel extractions stage

Oct. 8, 2007

Yusuf

  • Mini prep o/n of the following:
    • E1B# 1 -> A&B
    • E1B# 2 -> A&B
  • Mini prep of the following:
    • N2 -> A,B,C,D
    • R0062 -> C,D,E,F
  • The above mini preps kept in the igem box labelled with green sticker "DNA from plates"

TO DO:

  • Make
    • 5 AMP plates
    • 5 KAN Plates
    • 3 AMP+KAN Plates
  • Mini prep of:(in incubator)
    • E1B# 1 -> A&B
    • E1B# 2 -> A&B
  • Length Check for:
    • E1B# 1 -> A&B
    • E1B# 2 -> A&B
    • N2 -> A,B,C,D
    • R0062 -> C,D,E,F
  • Plasmid Digest and gel extract of the above constructs

Oct. 7, 2007

Esther, Conrad, Adnan

Done:

  • Transform E1b - Done with AMP plates. Two plates of this in the incubator. One may have been unsuccessful.
  • MP I13033A and J06801A (two each; also freezer stocks of these, one each), MP of I13504 A, B.
    • Label may have been switched between the two parts. Run a sample PD to check before proceeding.
      • The two that may have been switched are I13033A and J06801A - the ones that have the resistances written on them. The other ones were done later and there should be no problems.
  • MP o/n for N2 (4 colonies: A,B,C,D) and R0062 (colonies: C, D, E, F)

To Do:

  • MP O/N of E1b
  • MP of N2 (A,B,C,D) and R0062 (C,D,E,F)
  • Digest, GE, purify, quantitate:
    • I13033 A, S/P
    • J06801 A, E/X
    • Q04400 C, X/P (assuming R0011 was cut with S/P)
  • PD length check I13504 AB

Note: We are out of EtBr. Check with Seema.

Oct. 6, 2007

Anam, Tara, Jovan

  • Finished gel purification of J06801, J31003, B0034, E0433, I13033
  • MP for Q04400CD, R0062AB
  • PD length check for Q04400 CD, R0062AB
Part NamePartPlasmid
R0062 AXX
R0062 BXX
Q04400 COO
Q04400 DXX
  • Quantitation of J06801, J31003, B0034, E0433, I13033
    • Nothing showed up for J06801, I13033
    • [J31003] = 2.2 ng/uL
    • [B0034] = 9.4 ng/uL
    • [E0433] = 13.5 ng/uL
  • Ligated B0034 + J31003 = E1b (refer to diagram posted up in wet lab area)
  • Transformed N1A + S01003D = N2 and its in incubator.
  • MP o/n for I13033A (2 copies), J06801A (2 copies), I13504 AB in incubator. (2 copies should be combined into 1 Eppendorf tube each; should end up with 1 new miniprep of I13033A and J06801A. If these MPs are successful, remove/store the old ones)


TO DO:

  • Transform E1b
  • MP I13033A, and J06801A (and make stock if there isn't any in the -80 freezer of this)
    • Don't do PD length check on these because it has already been done before and has passed it.
  • Digest, GE, purify, quantitate:
    • I13033 A, S/P
    • J06801 A, E/X
    • Q04400 C, X/P (assuming R0011 was cut with S/P)
  • MP and PD length check I13504 AB
  • MP o/n for N2 (4 colonies: A,B,C,D)

Oct. 5, 2007

Yusuf, Maria, Talal, Faareha

SUMMARY:

  • Miniprep: J06801 (2005), Q04400 (2005), B0034 (2007), J31005 (2007)
  • Length Check:
Part NamePartPlasmid
B0034 AOO
B0034 BOO
J06801 AOO
J06801 BOO
J31005 AOO
J31005 BOO
Q04400 AOO
Q04400 BOO
  • Made competent cells
  • Ligate N1 A + S01003 D = N2 (overnight)
  • Made o/n of R0062 (2007) AB, Q04400 (2005) with high [IPTG] (pSB2k3 is high copy number in LacI- environment)
  • Transformed I13504 (2007)
  • Gel Extract:
    • B0034 A, S/P
    • E0433 A, X/P
    • I13033 A, S/P
    • J06801 A, E/X
    • J31003 A, X/P

TO DO:

  • B0015 (2005) didn't transform, try again
  • Complete gel extract procedure
  • Ligate:
    • B0034 A + J31003 A
    • I13033 A + E0433 A
    • (J23100 + S01640) D + J06801 A

Oct. 4, 2007

Esther, Neha, Rafsan

SUMMARY:

  • Found alternate to I1303: ligate terminator (B0015) and Lux pR promoter (R0062) separately
  • Transformed R0062 (2007), B0015 (2005)
  • Made o/n of DH5a, DH5a-z1, J06801 (2005), Q04400 (2005), B0034 (2007), J31005 (2007)
  • Digest and Gel Extract of N1 A with enzymes S/P
  • Quantitation: N1 = 16.8 ng/uL, S01003 (2007) = 4.1 ng/uL

TO DO:

  • Make o/n: R0062 (2007), B0015 (2005)
  • Miniprep and Check Lengths: J06801 (2005), Q04400 (2005), B0034 (2007), J31005 (2007)
  • Ligate N1 and S01003 and transform in DH5a
  • Make competent cells

Oct. 3, 2007

Yusuf

SUMMARY:

  • Transformed: J06801 (2005), Q04400 (2005), B0034 (2007), J31005 (2007)
  • Minipreped I130033 AB, E0433 AB, S03140 AB, J04500 AB, J31003 AB, N1 AB
  • Made o/n of DH5a and DH5a-z1 (from July 16 plate - ask Seema if this is ok)
  • Length Check (O = match, X = does not match):
Part NamePartPlasmid
E0433 AOO
E0433 BOO
I13033 AXO
I13033 BXO
J04500 AOO
J04500 BOO
J31003 AOO
J31003 BOO
N1 AOO
N1 BOO
S03140 AOO
S03140 BOO

TO DO:

  • Make 5 Kan plates
  • Make bottle of LB Broth
  • Make competent cells
  • Make o/n of J06801 (2005), Q04400 (2005), B0034 (2007), J31005 (2007)
  • Ligate N1 + S01003
  • Find alternate to I13033

Oct. 2, 2007

Natalie

SUMMARY:

  • Made o/n (2 each) of: I130033 AB, E0433 AB, S03140 AB, J04500 AB, J31003 AB, N1 AB
  • NOTE: N1 = J23100 C + S01640 B + B0015

TO DO:

  • Miniprep all above parts and length check
  • Transform:
    • J06801 (2005) - it's in the source box (this is a larger composite part containing J06501)
    • B0034 - also in source box, if not, get it from Registry plates
    • Q04400 - re-transform using more DNA to see if we get more colonies and transform 2005/2006 version in the source box
    • J31005 - chloramphenicol resistance, just in case we need it
  • Continue cataloging and organization (Charles: I'll be dropping by to help out with that)

Oct. 1, 2007

Time: 3:45 PM - 8:30 PM

Yusuf, Irina

Summary:

  • made 5 KAN plates
  • made 2 AMP+KAN plates
  • made 300 mL LB

Tranformation of following parts:

  • I13033 -> KAN
  • E0433 -> KAN
  • S03140 -> AMP
  • J04500 -> KAN
  • J31003 -> AMP
  • (J23100C + S01640B)+ B0015 -> KAN

Used 4uL of DNA for all transformations

  • tried to do DNA extraction for J06501 but somebody already extracted it (wasn't in the well)
  • couldn't find it in the igem dna box as well !!!

TO DO:

  • MP o/n for the above parts
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