Team:METU HS Ankara/Notebook

Notebook

Wednesday , October 14th

Dry Lab: Tasks and duties were distributed

Wednesday , October 21st

Dry Lab: Project topic was discussed

Wednesday , October 28th

Dry Lab: Researchs for our project started

Wednesday , November 18th

Dry Lab: Researchs continiued

Wednesday , November 25th

Dry Lab: Human practice was discussed

Wednesday , December 2nd

Dry Lab: Human practice was discussed, DNA Day was planned

Wednesday , December 9th

Dry Lab: Human practice was discussed
Wet Lab : Preperation for lab started

Wednesday , December 16th

Wet Lab : Lab rules, safety and protocols were revised
Dry Lab: Researches were discussed

Wednesday , December 23rd

Dry Lab: Parts were taught
Wet Lab : Lab protocols were revised

Wednesday , January 13rd

Dry Lab: Project topic was decided
Researchs about cancer started

Saturday , January 23rd

Dry Lab: Cancer cell line were taught
Research about gene sequences of cancer inhibitors started

Wednesday , February 10th

Dry Lab: Project topic was spesified
Researchs for our project continiued ( detailed research about colon cancer )

Saturday , February 13rd

Wet Lab : First day of lab . Lab supplies were introduced.
Dry Lab: Parts were discussed ( 2015 Harvard Team's Parts)
Researchs for our project continiued

Wednesday , February 17th

Dry Lab: Sequence for our project was designed ( draft )
Researches about Butyric Acid started

Friday , February 26th

Dry Lab: Parts were discussed
Sequence for our project was specified

Saturday , March 5th

Dry Lab: Human practice was discussed
DNA Day was planned

Wednesday , March 9th

Dry Lab: First Quiz was made ( about digestion & ligation )

Wednesday , April 13rd

Dry Lab: Collaboration was discussed

Wednesday April 20th

Dry Lab: Wiki tasks were distributed

Saturday , May 7th

Wet Lab : E0240 : 876 bp / Chl / RBS+GFP+Double Terminator
Groups

35 bp/ JL23116/Prom. -Chl
64 bp/ B0010/Terminator-Chl
876 bp/ E0240/ RBS+Gene+D. -Chl
1687 bp/ I742111/RBS+Limone Synthase- Chl
12 bp/ BOO34/ RBS-Chl

Saturday , May 14th

Wet Lab : Transformation , selective culturing , plasmid isolation , digestion , gel scanning were taught
Biodrop was made
Gel preparation was made

130 mL TAE Buffer
1.3 Agarose

Criterias for Digestion

Order of sequence
base pairs
insert-vector

Double Digestion

10 µL Plasmid
6 µL MGW (water)
1 µL Buffer 1
1 µL Buffer 2
1 µL Enzyme 1
1 µL Enzyme 2

Single Digestion

10 µL Plasmid
8 µL MGW (water)
1 µL Buffer 1
1 µL Enzyme 1

2 gel type;
100-1000 bp
500-5000 bp

LB Broth 25 gr/1L
LB Agar 40 gr/1L

Saturday , May 28th

Wet Lab : Transformation was made ( no results ) E0240 (Chl)
Dry Lab: Wiki page preparation started

Saturday , June 4th

Wet Lab : Transformation of J23116 etc.

Monday , June 13rd

Dry Lab: Human practice was discussed
Collaboration was discussed

Tuesday , June 14th

Dry Lab: Survey about colon cancer was made.
Wet Lab : Dishes were cleaned, LB and Agar were sent to autoclav , competent preparation was made

Wednesday , June 15th

Wet Lab : Parts : E0240 , K808000 , R0010 - Chl
Autoclave at 2:50

Friday , June 17th

Wet Lab : Parts : K185010 & K185011 - Plasmid Isolation was made
ONC-3.colony,BL21

Saturday , June 18th

Wet Lab : Parts : R0010 , K808000 - Plasmid Isolation - ONC - Nanodrop - Digestion was made
Part : E0240 - Nanodrop , Digestion ,ONC will be made

Friday, June 24th

E0240, K808000, R0010, K1850011, K1850010 (transformed+ P.I)
New Construct transformation
ONC of New Construct Plasmid isolation Pet 28a and E0240
Primer design of K1850010 and K1850011
Digestion of Pet28a
Double digestion

Saturday , June 25th

Plasmid isolation of 3rd and 4th colony from new construct

Sunday , June 26th

Gel extraction, nanodrop and digestion of Pe28a and New Construct 3
1 hour 37° incubation

Monday , June 27th

ONC of New Construct andPet28a
Ligation

Tuesday , June 28th

ONC of New Construct 3 and Pet28a and then plasmid isolation of them.
Nanodrop of them.
Ligation transformation.

Wednesday , June 29th

Transformation of 2 colonies and then ONC of them.
Gel extraction then nanodrop.

Thursday , June 30th

Gel extraction and nanodrop of the colonies from 29.06.2016

Monday , July 11th

Gel extraction of PsB1C3 and insert from E0240 and New Construct
Nanodrop results

Digestion ( E,P ) of NC-6 , NC-7 , E0240 1 AIB , E0240 2 AIB
Göksu , Zeynep
Researchs

Tuesday , July 12th

New ligation calculations of psB1C3 and Pet28a

Digestion, Autoclave , Alkaline phosphatase were made.
Ligation : 2/2 , 1/1 , 4/2 , 2/1 , 3/2 , 1/2

Dilara , Göksu ,Özgür ,Ece , Gizem , Duygu
Nanodrop Results ( ng / ml )

Ligation Calculations ( ng / ml )
psb1c3 , NC ( E.P )

~ 2.1
12 insert
5 vector

Thursday , July 14th

Digestion of;
New construct- 6th colony
New Construct- 7th colony
Pet28a- 1st colony

ONC preparation , plasmid isolation , gel electrophoresis , gel extraction were made.
Nanodrop results

Transformation

Plasmid isolation
Nanodrop results

Tuesday - Wednesday , July 26th - 27th

Sterilazation of tips and MGW
Preparation of new plates.
Spread the cells on plates of K1850010, K1850011, K1850013 and then plasmid isolation of them.
Primer design and PCR
Strick plate of previous ligation transformations.
Digestion and ligation from pet28a and New construct. (SalI and HindIII)
ONC of previous ligations (S,H)
Plasmid isolation of them and nanodrop.

Gel extraction.

ONC was made – NC , pet28a , psb1c3
Digestion was made
Primer design was made
LB Agar was prepared

Thursday , July 28th

Nanodrop of; New Construct, pet28a, psB1C3.

Plasmid isolation of NC1, pet28a , K881000
Digestion 2

Friday , July 29th

Ligation transformations of;
Transformation of
Single cut of C1, C2 , C3, C4
Single cut of S,H ligation transformations Onc’s gel extraction.

Monday , August 1st

Double cut with EcoRI and Pst1 of K1850013, K1850010, K1850011
Single digestion of S,H lig PI
Double digestion of K1850011, K1850013
ONC of New Construct, pet28a, K808000, K1850010, K1850011, K1850013

Plasmid isolation
Single digestion
ONC and PI
Nanodrop results

Digestion Single ( S,H lig ) – Double ( K1850011 , K1850013 )

Tuesday , August 2nd

Plasmid isolation of K808000, New Construct, K1850013, K1850011, K1850010, pet28a, Sh lig
Ligation of new construct+ pet28a by NcoI and HindIII and new construct+ pet28a by SalI and HindIII
Plasmid Isolation

Nanodrop results

Digestion

Wednesday , August 3rd

Digestion of new construct 6mL and 8 mL which are cut with EcoRI and PstI. (buffer-cutsmart)

Thursday , August 4th

Plasmid isolation of previous ONC.
Tansformed ligation ONC preparaion of 2 mL instead of 5 mL.

Friday , August 5th

ONC of 5x cullture New Construct, pet28a, psB1C3, K808000, BL21,N.H lig
Plasmid isolation and nanodrop

Monday , August 8th

*Plasmid isolation of BL21 and pet28a colonies 1,2,3
*Digestion of
Nc- E,S and X,P
K1850013-E,S and X,P
NCI- E,X,S,P
*Digestion of pet28a BL21 ; 1,2 (HindIII) ,3
*ONC of NCI, NC2 and pet28a
*Gel extraction of K1850013, NCI,pet28a