iGEM 2016 — Team METU_HS_Ankara

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# Team:METU HS Ankara/Notebook

### [![metuhs](https://static.igem.org/mediawiki/2016/5/50/T--METU_HS_Ankara--logoo.png)](index.html "Home")

* [Home](https://2016.igem.org/Team%3AMETU_HS_Ankara)
* Team
  + [Team](https://2016.igem.org/Team%3AMETU_HS_Ankara/Team)
  + [Collaborations](https://2016.igem.org/Team%3AMETU_HS_Ankara/Collaborations)
* [Project](#slider_meetup)
  + [Description](https://2016.igem.org/Team%3AMETU_HS_Ankara/Description)
  + [Design](https://2016.igem.org/Team%3AMETU_HS_Ankara/Design)
  + [Experiments](https://2016.igem.org/Team%3AMETU_HS_Ankara/Experiments)
  + [Proof of Concept](https://2016.igem.org/Team%3AMETU_HS_Ankara/Proof)
  + [Demonstrate](https://2016.igem.org/Team%3AMETU_HS_Ankara/Demonstrate)
  + [Results](https://2016.igem.org/Team%3AMETU_HS_Ankara/Results)
  + [Notebook](https://2016.igem.org/Team%3AMETU_HS_Ankara/Notebook)
* [Parts](#agenda)
  + [Basic Parts](https://2016.igem.org/Team%3AMETU_HS_Ankara/Basic_Part)
  + [Composite Parts](https://2016.igem.org/Team%3AMETU_HS_Ankara/Composite_Part)
  + [Part Collection](https://2016.igem.org/Team%3AMETU_HS_Ankara/Part_Collection)
* [Model](https://2016.igem.org/Team%3AMETU_HS_Ankara/Model)
* [Attributions](https://2016.igem.org/Team%3AMETU_HS_Ankara/Attributions)
* [Human Practice](https://2016.igem.org/Team%3AMETU_HS_Ankara/Human_Practices)
* [Safety](https://2016.igem.org/Team%3AMETU_HS_Ankara/Safety)
* [Achievements](https://2016.igem.org/Team%3AMETU_HS_Ankara/Achievements)
* [Gallery](https://2016.igem.org/Team%3AMETU_HS_Ankara/Gallery)

#### Notebook

#### Wednesday , October 14th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Dry Lab: Tasks and duties were distributed

#### Wednesday , October 21st

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Dry Lab: Project topic was discussed

#### Wednesday , October 28th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Dry Lab: Researchs for our project started

#### Wednesday , November 18th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Dry Lab: Researchs continiued

#### Wednesday , November 25th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Dry Lab: Human practice was discussed

#### Wednesday , December 2nd

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

#### Wednesday , December 9th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

#### Wednesday , December 16th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

#### Wednesday , December 23rd

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

#### Wednesday , January 13rd

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Dry Lab: Project topic was decided
Researchs about cancer started

#### Saturday , January 23rd

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

#### Wednesday , February 10th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

#### Saturday , February 13rd

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

![](https://static.igem.org/mediawiki/2016/5/5a/T--METU_HS_Ankara--n01.jpg)

#### Friday , February 26th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

![](https://static.igem.org/mediawiki/2016/3/3f/T--METU_HS_Ankara--n02.jpg)

#### Saturday , March 5th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Dry Lab: Human practice was discussed
DNA Day was planned

#### Wednesday , March 9th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

#### Wednesday , April 13rd

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Dry Lab: Collaboration was discussed

#### Wednesday April 20th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Dry Lab: Wiki tasks were distributed

#### Saturday , May 7th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

![](https://static.igem.org/mediawiki/2016/9/93/T--METU_HS_Ankara--nt01.jpg)

#### Saturday , May 28th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Wet Lab : Transformation was made ( no results ) E0240 (Chl)

Dry Lab: Wiki page preparation started

#### Saturday , June 4th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Wet Lab : Transformation of J23116 etc.

#### Monday , June 13rd

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Dry Lab: Human practice was discussed
Collaboration was discussed

#### Tuesday , June 14th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

![](https://static.igem.org/mediawiki/2016/8/83/T--METU_HS_Ankara--nt02.jpg)

#### Friday , June 17th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Wet Lab : Parts : K185010 & K185011 - Plasmid Isolation was made

ONC-3.colony,BL21

#### Saturday , June 18th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Wet Lab : Parts : R0010 , K808000 - Plasmid Isolation - ONC - Nanodrop - Digestion was made

Part : E0240 - Nanodrop , Digestion ,ONC will be made

![](https://static.igem.org/mediawiki/2016/9/9b/T--METU_HS_Ankara--nt03.jpg)

#### Friday, June 24th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

#### Sunday , June 26th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

#### Monday , June 27th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

ONC of New Construct andPet28a
Ligation

#### Tuesday , June 28th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

#### Wednesday , June 29th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

#### Thursday , June 30th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Gel extraction and nanodrop of the colonies from 29.06.2016

#### Monday , July 11th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

![](https://static.igem.org/mediawiki/2016/8/8e/T--METU_HS_Ankara--nt04.jpg)

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

![](https://static.igem.org/mediawiki/2016/5/5e/T--METU_HS_Ankara--nt05.jpg)

#### Tuesday , July 12th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

New ligation calculations of psB1C3 and Pet28a

![](https://static.igem.org/mediawiki/2016/6/65/T--METU_HS_Ankara--nt06.jpg)

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 )

![](https://static.igem.org/mediawiki/2016/d/da/T--METU_HS_Ankara--nt07.jpg)

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

![](https://static.igem.org/mediawiki/2016/6/63/T--METU_HS_Ankara--nt08.jpg)

~ 2.1
12 insert
5 vector

#### Thursday , July 14th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

![](https://static.igem.org/mediawiki/2016/8/8a/T--METU_HS_Ankara--nt09.jpg)

Transformation

Plasmid isolation
Nanodrop results

![](https://static.igem.org/mediawiki/2016/8/81/T--METU_HS_Ankara--nt10.jpg)

Plasmid isolation
Nanodrop results

![](https://static.igem.org/mediawiki/2016/b/bf/T--METU_HS_Ankara--nt11.jpg)

#### Tuesday - Wednesday , July 26th - 27th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

* 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

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Nanodrop of; New Construct, pet28a, psB1C3.

![](https://static.igem.org/mediawiki/2016/9/94/T--METU_HS_Ankara--nt12.jpg)

* Plasmid isolation of NC1, pet28a , K881000
* Digestion 2

![](https://static.igem.org/mediawiki/2016/a/a0/T--METU_HS_Ankara--nt13.jpg)

#### Friday , July 29th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

* Ligation transformations of;
* ![](https://static.igem.org/mediawiki/2016/c/c1/T--METU_HS_Ankara--nt14.jpg)
* Transformation of
* ![](https://static.igem.org/mediawiki/2016/8/82/T--METU_HS_Ankara--nt15.jpg)
* Single cut of C1, C2 , C3, C4
* Single cut of S,H ligation transformations Onc’s gel extraction.

#### Monday , August 1st

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

* 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

![](https://static.igem.org/mediawiki/2016/a/a1/T--METU_HS_Ankara--nt16.jpg)

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

#### Tuesday , August 2nd

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

![](https://static.igem.org/mediawiki/2016/3/3d/T--METU_HS_Ankara--nt17.jpg)

Nanodrop results

![](https://static.igem.org/mediawiki/2016/a/a5/T--METU_HS_Ankara--nt18.jpg)

Digestion

![](https://static.igem.org/mediawiki/2016/2/2d/T--METU_HS_Ankara--nt19.jpg)

#### Wednesday , August 3rd

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

![](https://static.igem.org/mediawiki/2016/d/d8/T--METU_HS_Ankara--nt20.jpg)

#### Thursday , August 4th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

#### Friday , August 5th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

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

![](https://static.igem.org/mediawiki/2016/d/d1/T--METU_HS_Ankara--nt21.jpg)

#### Monday , August 8th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

\*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

#### Wednesday , August 10th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

ONC of New Construct

![](https://static.igem.org/mediawiki/2016/6/6c/T--METU_HS_Ankara--nt22.jpg)

#### Thursday , August 11th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

New Construct transformation to Amp resistance plate

![](https://static.igem.org/mediawiki/2016/8/86/T--METU_HS_Ankara--nt23.jpg)

![](https://static.igem.org/mediawiki/2016/d/df/T--METU_HS_Ankara--nt24.jpg)

#### Monday , August 22nd

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

New Construct transformation to Amp resistance plate

![](https://static.igem.org/mediawiki/2016/4/49/T--METU_HS_Ankara--nt25.jpg)

#### Tuesday , August 23rd

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Plasmid Isolation

![](https://static.igem.org/mediawiki/2016/5/5e/T--METU_HS_Ankara--nt26.jpg)

Gel Extraction

* I1200 à 4 ng/µl
* I1500 (X,P) à 17,5 ng/µl

16h digestions were gel imaged
Gel Extraction

![](https://static.igem.org/mediawiki/2016/1/13/T--METU_HS_Ankara--nt27.jpg)

Digestion
Transformation

* L1) NC+psBC1 à Chl
* L2) NC + psBC2 à Chl
* L3) NC + pet28a à Kana

Gel Imaging

* D1
* D2
* D3

Ligation

* L4) NC (E,S) / K1850010 (E,S)
* L5) NC (X,P) / K1850010 (X,P)
* L6) NC3 (E,S) / pSBC3 (X,P)
* L7) NC3 (X,P) / pSBC3 (X,P)

Gel Extraction

![](https://static.igem.org/mediawiki/2016/a/a9/T--METU_HS_Ankara--nt28.jpg)

#### Wednesday , August 24th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Ligation
Digestion
Transformation
Plasmid Isolation

![](https://static.igem.org/mediawiki/2016/e/e7/T--METU_HS_Ankara--nt29.jpg)

Digestion

* SH Lig1
* SH Lig2

#### Thursday , August 25th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Transformation

* L8, L9, L10, L11→ Chl
* SH Lig PI 1&2 → Kana
* B0010 → Amp

Gel Imaging
Gel Extraction
Ligation

#### Friday , August 26th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Gel Imaging
Digestion

#### Saturday , August 27th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Plasmid Isolation
Gel Extraction
Nanodrop Results

![](https://static.igem.org/mediawiki/2016/6/66/T--METU_HS_Ankara--nt30.jpg)

Ligation
Digestion

* D11) NC (X,P) 1500 bp
* D12) NC (E,S) 1200 bp
* D13) pSB (X,P) 2100 bp
* D14) pSB (E,S) 2100 bp

ONC

#### Sunday , August 28th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Plasmid Isolation

![](https://static.igem.org/mediawiki/2016/4/4f/T--METU_HS_Ankara--nt31.jpg)

Gel Imaging
Single Digestion
Transformation

#### Tuesday , August 30th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Ligation
Digestion

#### Wednesday , August 31st

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Gel Extraction
Ligation

* L27 → Kana
* L28 → Kana
* L29 → Chl
* L30 → Chl

#### Friday , September 2nd

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Plasmid Isolation

![](https://static.igem.org/mediawiki/2016/e/e6/T--METU_HS_Ankara--nt32.jpg)

#### Saturday , September 3rd

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Single digestion of L23C1, L23C2 EcorI
Plasmid Isolation of L23, L25, L26

![](https://static.igem.org/mediawiki/2016/9/95/T--METU_HS_Ankara--nt33.jpg)

Transformation of L27, L28,L29,L30
Gel control L23 Col1 and L23 Col2 has accurate results.
L23, L25, L26; ONC

#### Sunday , September 4th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Digestion

![](https://static.igem.org/mediawiki/2016/c/c7/T--METU_HS_Ankara--nt34.jpg)

DH5α, L27, L28 ONC

#### Monday , September 5th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

DH5α competent preparation
S,H and N,S digested NC and pet28a gel control
S,H plasmid isolation
PCR confirmation (X,P and E,S)

#### Tuesday , September 6th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Gel extraction (S,H)
Transformation

* L25, L26 (Kana)
* Device 1,2,3 (Chl)
* RFP (Chl, Kana)
* J2300 (Chl, Amp)

#### Thursday , September 8th

![line](https://static.igem.org/mediawiki/2016/3/3e/T--METU_HS_Ankara--line.jpg)

Ligation of pet28a and NC S,H digestion
S,H and N,S digestion to Pet28a & NC
S digestion to pet28a PI.

![](https://static.igem.org/mediawiki/2016/c/c0/T--METU_HS_Ankara--nt35.jpg)

Digestion

* D44 NC (10microliters) N,S
* D45 Pet28a (10microliters) N,S
* D46 NC (10microliters) H
* D47 Pet28a (10microliters) H

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