Ann's Notebook

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= '''<font color= mediumblue size=6>Ann's Notebook</font>''' =
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[[media:6_19_09_Media_recipes.pdf| 6/19/09 and 6/25/09]]
 +
*M9 salts
 +
*Liquid LB
 +
*Antibiotic stock solutions
 +
*LB plates
 +
[[media:7_22_09_and_7_23_09_Transformation_of_RBS_for_Pu_and_Killer_genes.pdf| 7/22/09 and 7/23/09]]
[[media:7_22_09_and_7_23_09_Transformation_of_RBS_for_Pu_and_Killer_genes.pdf| 7/22/09 and 7/23/09]]
*Media preparation for transformation
*Media preparation for transformation
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*Nanodrop concentrations of the RBS for Pu promoter, Bacteriophage lysis cassette, lambda lysis device, T4 lysis device
*Nanodrop concentrations of the RBS for Pu promoter, Bacteriophage lysis cassette, lambda lysis device, T4 lysis device
*Digestion of the RBS for Pu promoter and the Bacteriophage lysis cassette
*Digestion of the RBS for Pu promoter and the Bacteriophage lysis cassette
 +
 +
[[media:7_27_09_Gel_of_RBS_and_Bacteriophage_lysis_cassette_digest_Plates_for_Pu_promoter_colony_PCR_Streaking_out_Pu_luciferase_part_from_the_registry.pdf| 7/27/09]]
 +
*Plated overnight cultures for Pu colony PCR
 +
*Protocol for running a gel
 +
*Ran gel of the RBS for Pu promoter and Bacteriophage lysis cassette
 +
*Plated Pu-luciferase part sent from the registry
 +
 +
[[media:7_28_09_Frozen_stock_Pu_luciferase_and_digest_of_lambda_T4_killer_genes.pdf| 7/28/09]]
 +
*Overnight culture for frozen stock of Pu-luciferase biobrick
 +
*Digest of lambda and T4 killer genes to check part length with EcoRI, PstI, BglII and EcoRI/BglII
 +
 +
[[media:7_29_09_Frozen_stock_Pu_luciferase_gel_of_lambda_and_T4_digest_of_lambda_and_T4.pdf| 7/29/09]]
 +
*Frozen stock of Pu-luciferase biobrick
 +
*Gel of lambda and T4 killer genes digested with EcoRI, PstI, BglII and EcoRI/BglII
 +
*Digest of lambda and T4 killer genes with EcoRI/PstI, EcoRI/XhoI, XhoI
 +
 +
[[media:7_30_09_gel_of_lambda_and_T4_killer_gene_and_gel_of_pu_colony_pcr.pdf| 7/30/09]]
 +
*Gel of lambda and T4 killer genes digested with EcoRI/PstI, EcoRI/XhoI, XhoI
 +
*Gel of Pu promoter colony PCR
 +
 +
[[media:8_3_09_Analysis_of_Pu_promoter_colony_PCR.pdf| 8/3/09]]
 +
*Analysis of Pu promoter colony PCR
 +
**Primer sequence
 +
**PCR conditions
 +
 +
[[media:8_4_09_Pu_Promoter_colony_PCR_and_HPLC_investigation.pdf| 8/4/09]]
 +
*Protocol for colony PCR
 +
*Colony PCR for Pu Promoter
 +
*Gel of Colony PCR for Pu promoter with samples at different annealing temperatures
 +
*Meeting with Pablo about HPLC
 +
 +
[[media:8_5_09_Pu_promoter_colony_PCR_optimization,_Pu_promoter_purification_and_nanodrop.pdf| 8/5/09]]
 +
*Protocol for DNA purification
 +
*DNA purification of Pu promoter colony PCR
 +
*Optimization of Pu promoter colony PCR
 +
*Nanodrop of Pu promoter
 +
 +
[[media:8_6_09_Pu_Promoter_DNA_concentration_and_nanodrop.pdf| 8/6/09]]
 +
*Protocol for DNA precipitation
 +
*DNA concentration of Pu promoter
 +
*Nanodrop results for concentrated Pu promoter
 +
 +
[[media:8_8_09_Transformation_of_GFP_generator.pdf| 8/8/09]]
 +
*Comp. cell preparation and transformation of a GFP generator
 +
 +
[[media:8_9_09_Miniprep_and_nanodrop_GFP_generator_colony_PCR_pu_promoter_round_2_nanodrop_digest_for_pu_gfp_with_leu_landing_pad.pdf| 8/9/09]]
 +
*Pu promoter colony PCR round 2
 +
*Gel of Pu promoter colony PCR round 2
 +
*DNA purification of colony PCR round 2
 +
*Nanodrop of colony PCR round 2 and leu landing pad
 +
*Miniprep of GFP generator
 +
*Nanodrop of GFP generator
 +
*Digest for Pu-RBS-GFP
 +
 +
[[media:8_10_09_Gel_of_digested_Pu_GFP_Leu_LP.pdf| 8/10/09]]
 +
*Gel of digest for Pu-RBS-GFP
 +
 +
[[media:8_11_09_Digest_and_gel_of_GFP_gen_Pu_prom_round_3_PCR_gel_and_nanodrop.pdf| 8/11/09]]
 +
*Digest of GFP generator
 +
*Gel of GFP generator
 +
*Pu promoter colony PCR round 3
 +
*Gel of Pu promoter colony PCR round 3
 +
*DNA purification of Pu promoter colony PCR round 3
 +
*Nanodrop of Pu promoter colony PCR round 3
 +
 +
[[media:8_12_09_Digest_Pu_round_3_DNA_purification_and_nanodrop_of_Pu_GFP_digests.pdf| 8/12/09]]
 +
*Pu promoter round 3 digestion
 +
*DNA purification of digest for Pu-RBS-GFP
 +
*Nanodrop of digest for Pu-RBS-GFP
 +
 +
[[media:8_13_09_Pu_GFP_leu_LP_preparations_for_ligation.pdf| 8/13/09]]
 +
*Gel of purified DNA for digest round 1
 +
*Digest of DNA for Pu-RBS-GFP ligation round 2
 +
*Trouble shooting DNA purification process
 +
*Gel of digested Pu, GFP, leu LP round 2
 +
*DNA purification of digested Pu, GFP, leu LP round 2
 +
*Nanodrop of digested Pu, GFP, leu LP round 2
 +
 +
GRE/VACATION
 +
 +
[[media:9_8_09_Pu_GFP_leu_landing_pad_ligation.pdf| 9/8/09]]
 +
*ligation protocol
 +
*Pu-GFP-leu landing pad ligation
 +
 +
[[media:9_9_09_ATCC_sodium_benzoate_plate_and_liquid_media.pdf| 9/9/09]]
 +
*ATCC sodium benzoate plate and liquid media recipes
 +
*Media prep for transformation of Pu GFP leu landing pad
 +
 +
[[media:9_10_09_and_9_11_09_Transformation_of_Pu_GFP_leu_ligation.pdf| 9/10/09 and 9/11/09]]
 +
*Comp. cell preparation and transformation of Pu GFP leu landing pad ligation into E. coli and P. putida mt-2 (with TOL plasmid)
 +
 +
[[media:9_12_09_Pu_GFP_leu_transformation_results.pdf| 9/12/09]]
 +
*Pu GFP leu landing pad transformation results
 +
*Start overnight cultures for Pu GFP leu landing pad miniprep
 +
 +
[[media:9_22_09_Team_Meeting_Project_modifications.pdf| 9/13/09]]
 +
*Pu GFP leu landing pad transformation results
 +
*Start overnight cultures for Pu GFP leu landing pad miniprep
 +
 +
[[media:9_14_09_Nanodrop_and_digest_of_miniprepped_Pu_GFP_leu_ligations.pdf| 9/14/09]]
 +
*Nanodrop of Pu GFP leu landing pad miniprep
 +
*Digest of Pu GFP leu landing pad with EcoRI to determine the plasmids with the insert
 +
 +
[[media:9_15_09_Gel_of_Pu_GFP_leu_ligation_digestion_with_EcoRI_product.pdf| 9/15/09]]
 +
*Gel of Pu GFP leu landing pad ligation miniprepped products digested with EcoRI
 +
 +
[[media:9_16_2009_digest_of_ligated_Pu_GFP_leu_with_EcoRI_round_2.pdf| 9/16/09]]
 +
*Gel of Pu GFP leu landing pad ligation miniprepped products digested with EcoRI round 2
 +
 +
[[media:9_18_09_Primer_Design_for_Sequencing_of_Pu_GFP_leu.pdf| 9/18/09]]
 +
*Primer design for sequencing of Pu GFP leu landing pad
 +
 +
[[media:9_22_09_Team_Meeting_Project_modifications.pdf| 9/22/09]]
 +
*Weekly team meeting: project modifications
 +
 +
[[media:10_2_09_Pr_XylR_Primers.pdf| 10/2/09]]
 +
*Protocol for primer design
 +
*Primer design for PrXylR
 +
 +
[[media:10_5_09_Colony_PCR_PrXylR.pdf| 10/5/09]]
 +
*Colony PCR PrXylR
 +
 +
[[media:10_6_09_gel_of_colony_PCR_PrXylR.pdf| 10/6/09]]
 +
*Gel of Colony PCR PrXylR
 +
 +
[[media:10_9_09_Protocol_for_gel_extraction,_gel_extraction_of_PrXylR.pdf| 10/9/09]]
 +
*Protocol for gel extraction
 +
*Gel extraction of PrXylR colony PCR
 +
*Nanodrop of PrXylR gel extraction
 +
*Gel of PrXylR gel extraction
 +
 +
[[media:10_10_09_PCR_amplification_of_gel_purification_Colony_PCR_of_Pu.pdf| 10/10/09]]
 +
*PrXylR PCR amplification from gel extraction
 +
*Revised Pu promoter colony PCR
 +
*Gel of PrXylR and Revised Pu promoter PCR
 +
 +
[[media:10_11_09_Purification_of_revised_pu_promoter_and_digest_for_ligation.pdf| 10/11/09]]
 +
*Purification of revised Pu promoter
 +
*Nanodrop of revised Pu promoter
 +
*Digest of revised Pu promoter and GFP generator
 +
 +
[[media:10_13_09_and_10_14_09_miniprep_of_leu_LP_digest_of_leu_LP_and_PrXylR.pdf| 10/13/09 abd 10/14/09]]
 +
*Miniprep of leu landing pad
 +
*Nanodrop of leu landing pad miniprep
 +
*Digest of leu landing pad and PrXylR
 +
*Gel of Digested Revised Pu, GFP generator, PrXylR, LeuLP and uncut Leu LP for ligation
 +
*Ligation of Pu/GFP and PrXylR/LeuLP
 +
 +
[[media:10_15_09_10_16_09_Transformation_of_PrXylR_and_Pu_GFP_ligation.pdf| 10/15/09 abd 10/16/09]]
 +
*Comp. cell prep and transformation of PrXylR/LeuLP and Pu/GFP
 +
 +
[[media:10_18_09_Miniprep_of_Pu_GFP_ligation_round_2_and_PrXylR_ligation.pdf| 10/18/09]]
 +
*Miniprep of Pu/GFP and 1 PrXylR transformation colony
 +
 +
[[media:10_19_09_Digest_and_gel_of_miniprepped_PuGFP_PrLeuLP_and_prep_for_submission_into_biobricks2.pdf| 10/19/09]]
 +
*Nanodrop of miniprepped Pu/GFP and PrXylR/LeuLP ligation products
 +
*Digestion of miniprepped Pu/GFP and PrXylR/LeuLP ligation products
 +
*Gel of digested Pu/GFP and PrXylR/LeuLP
 +
*Submitting Parts to the Registry

Latest revision as of 03:08, 22 October 2009


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HOME THE TEAM THE PROJECT MODELING REGISTRY PARTS NOTEBOOK SAFETY



Ann's Notebook


6/19/09 and 6/25/09

  • M9 salts
  • Liquid LB
  • Antibiotic stock solutions
  • LB plates

7/22/09 and 7/23/09

  • Media preparation for transformation
  • Comp. cell protocol
  • Protocol for getting parts from the biobricks
  • Transformation protocol
  • Transformation of RBS for Pu promoter, Bacteriophage lysis cassette, lambda lysis device, T4 lysis device

7/24/09

  • Protocol for miniprep
  • Miniprep of RBS for Pu promoter, Bacteriophage lysis cassette, lambda lysis device, T4 lysis device

7/25/09

  • Protocol for using the nanodrop
  • Protocol for a digestion
  • Nanodrop concentrations of the RBS for Pu promoter, Bacteriophage lysis cassette, lambda lysis device, T4 lysis device
  • Digestion of the RBS for Pu promoter and the Bacteriophage lysis cassette

7/27/09

  • Plated overnight cultures for Pu colony PCR
  • Protocol for running a gel
  • Ran gel of the RBS for Pu promoter and Bacteriophage lysis cassette
  • Plated Pu-luciferase part sent from the registry

7/28/09

  • Overnight culture for frozen stock of Pu-luciferase biobrick
  • Digest of lambda and T4 killer genes to check part length with EcoRI, PstI, BglII and EcoRI/BglII

7/29/09

  • Frozen stock of Pu-luciferase biobrick
  • Gel of lambda and T4 killer genes digested with EcoRI, PstI, BglII and EcoRI/BglII
  • Digest of lambda and T4 killer genes with EcoRI/PstI, EcoRI/XhoI, XhoI

7/30/09

  • Gel of lambda and T4 killer genes digested with EcoRI/PstI, EcoRI/XhoI, XhoI
  • Gel of Pu promoter colony PCR

8/3/09

  • Analysis of Pu promoter colony PCR
    • Primer sequence
    • PCR conditions

8/4/09

  • Protocol for colony PCR
  • Colony PCR for Pu Promoter
  • Gel of Colony PCR for Pu promoter with samples at different annealing temperatures
  • Meeting with Pablo about HPLC

8/5/09

  • Protocol for DNA purification
  • DNA purification of Pu promoter colony PCR
  • Optimization of Pu promoter colony PCR
  • Nanodrop of Pu promoter

8/6/09

  • Protocol for DNA precipitation
  • DNA concentration of Pu promoter
  • Nanodrop results for concentrated Pu promoter

8/8/09

  • Comp. cell preparation and transformation of a GFP generator

8/9/09

  • Pu promoter colony PCR round 2
  • Gel of Pu promoter colony PCR round 2
  • DNA purification of colony PCR round 2
  • Nanodrop of colony PCR round 2 and leu landing pad
  • Miniprep of GFP generator
  • Nanodrop of GFP generator
  • Digest for Pu-RBS-GFP

8/10/09

  • Gel of digest for Pu-RBS-GFP

8/11/09

  • Digest of GFP generator
  • Gel of GFP generator
  • Pu promoter colony PCR round 3
  • Gel of Pu promoter colony PCR round 3
  • DNA purification of Pu promoter colony PCR round 3
  • Nanodrop of Pu promoter colony PCR round 3

8/12/09

  • Pu promoter round 3 digestion
  • DNA purification of digest for Pu-RBS-GFP
  • Nanodrop of digest for Pu-RBS-GFP

8/13/09

  • Gel of purified DNA for digest round 1
  • Digest of DNA for Pu-RBS-GFP ligation round 2
  • Trouble shooting DNA purification process
  • Gel of digested Pu, GFP, leu LP round 2
  • DNA purification of digested Pu, GFP, leu LP round 2
  • Nanodrop of digested Pu, GFP, leu LP round 2

GRE/VACATION

9/8/09

  • ligation protocol
  • Pu-GFP-leu landing pad ligation

9/9/09

  • ATCC sodium benzoate plate and liquid media recipes
  • Media prep for transformation of Pu GFP leu landing pad

9/10/09 and 9/11/09

  • Comp. cell preparation and transformation of Pu GFP leu landing pad ligation into E. coli and P. putida mt-2 (with TOL plasmid)

9/12/09

  • Pu GFP leu landing pad transformation results
  • Start overnight cultures for Pu GFP leu landing pad miniprep

9/13/09

  • Pu GFP leu landing pad transformation results
  • Start overnight cultures for Pu GFP leu landing pad miniprep

9/14/09

  • Nanodrop of Pu GFP leu landing pad miniprep
  • Digest of Pu GFP leu landing pad with EcoRI to determine the plasmids with the insert

9/15/09

  • Gel of Pu GFP leu landing pad ligation miniprepped products digested with EcoRI

9/16/09

  • Gel of Pu GFP leu landing pad ligation miniprepped products digested with EcoRI round 2

9/18/09

  • Primer design for sequencing of Pu GFP leu landing pad

9/22/09

  • Weekly team meeting: project modifications

10/2/09

  • Protocol for primer design
  • Primer design for PrXylR

10/5/09

  • Colony PCR PrXylR

10/6/09

  • Gel of Colony PCR PrXylR

10/9/09

  • Protocol for gel extraction
  • Gel extraction of PrXylR colony PCR
  • Nanodrop of PrXylR gel extraction
  • Gel of PrXylR gel extraction

10/10/09

  • PrXylR PCR amplification from gel extraction
  • Revised Pu promoter colony PCR
  • Gel of PrXylR and Revised Pu promoter PCR

10/11/09

  • Purification of revised Pu promoter
  • Nanodrop of revised Pu promoter
  • Digest of revised Pu promoter and GFP generator

10/13/09 abd 10/14/09

  • Miniprep of leu landing pad
  • Nanodrop of leu landing pad miniprep
  • Digest of leu landing pad and PrXylR
  • Gel of Digested Revised Pu, GFP generator, PrXylR, LeuLP and uncut Leu LP for ligation
  • Ligation of Pu/GFP and PrXylR/LeuLP

10/15/09 abd 10/16/09

  • Comp. cell prep and transformation of PrXylR/LeuLP and Pu/GFP

10/18/09

  • Miniprep of Pu/GFP and 1 PrXylR transformation colony

10/19/09

  • Nanodrop of miniprepped Pu/GFP and PrXylR/LeuLP ligation products
  • Digestion of miniprepped Pu/GFP and PrXylR/LeuLP ligation products
  • Gel of digested Pu/GFP and PrXylR/LeuLP
  • Submitting Parts to the Registry
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