Team:Heidelberg/Notebook/miMeasure/September

From 2010.igem.org

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{| cellpadding="5" cellspacing="0" align="center" style="text-align: center; color:#4e93a4; border:1.53px solid #333333;"
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|- border="0"
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! colspan="7" style="background:#c85000;" | [http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/July<font color="white">July</font>]
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|- style="background:#c85000; color:white"
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|width="20pt"|'''M'''||width="20pt"|'''T'''||width="20pt"|'''W'''||width="20pt"|'''T'''||width="20pt"|'''F'''||width="20pt"|'''S'''||width="20pt"|'''S'''
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|colspan="3"| ||'''1'''||'''2'''||'''3'''||'''4'''
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|- style="background:#f2f2f2; color:#78b41e"
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|'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/July#05.2F07.2F2010 5]'''||'''6'''||'''7'''||'''8'''||'''9'''||'''10'''||'''11'''
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|- style="background:#f2f2f2; color:#78b41e"
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|'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/July#12.2F07.2F2010  12]'''||'''13'''||'''14'''||'''15'''||'''16'''||'''17'''||'''18'''
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|- style="background:#f2f2f2; color:#78b41e"
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|'''19'''||'''20'''||'''21'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/July#22.2F07.2F2010  22]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/July#23.2F07.2F2010 23]'''||'''24'''||'''25'''
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|- style="background:#f2f2f2; color:#78b41e"
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|'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/July#26.2F07.2F2010  26]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/July#27.2F07.2F2010 27]'''||'''28'''||'''29'''||'''30'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/July#31.2F07.2F20103 31]'''||colspan="1"|
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{| cellpadding="5" cellspacing="0" align="center" style="text-align: center; color:#009be1; border: 1.5px solid #000000;"
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|- border="0"
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! colspan="7" style="background:#f09600;" | [http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/August<font color="white">August</font>]
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|- style="background:#f09600; color:white"
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|width="20pt"|'''M'''||width="20pt"|'''T'''||width="20pt"|'''W'''||width="20pt"|'''T'''||width="20pt"|'''F'''||width="20pt"|'''S'''||width="20pt"|'''S'''
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|colspan="6"| ||'''1'''
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|- style="background:#f2f2f2; color:#009be1"
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|'''16'''||'''17'''||'''18'''||'''19'''||'''20'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/August#21/08/2010 21]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/August#22.2F08.2F2010 22]'''
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|- style="background:#f2f2f2; color:#009be1"
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|'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/August#23.2F08.2F2010 23]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/August#24.2F08.2F2010 24]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/August#25.2F08.2F2010 25]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/August#26.2F08.2F2010 26]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/August#27.2F08.2F2010 27]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/August#28.2F08.2F2010 28]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/August#29.2F08.2F2010 29]'''
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|- style="background:#f2f2f2; color:#009be1"
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|[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/August#302F08.2F2010 30]'''||[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/August#31.2F08.2F2010 31]'''||colspan="5"|
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|}
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{| cellpadding="5" cellspacing="0" align="center" style="text-align: center; color:#78b41e; border: 1.5px solid #333333;"
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|- border="0"
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! colspan="7" style="background:#009be1;" | [http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September<font color="#ffecba">September</font>]
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|- style="background:#009be1; color:white"
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|width="20pt"|'''M'''||width="20pt"|'''T'''||width="20pt"|'''W'''||width="20pt"|'''T'''||width="20pt"|'''F'''||width="20pt"|'''S'''||width="20pt"|'''S'''
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|- style="background:#f2f2f2; color:#78b41e"
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|colspan="2"| ||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#01.2F09.2F2010 1]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#02.2F09.2F2010 2]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#03.2F09.2F2010 3]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#04.2F09.2F2010 4]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#05.2F09.2F2010 5]'''
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|- style="background:#f2f2f2; color:#78b41e"
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|'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#06.2F09.2F2010 6]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#07.2F09.2F2010 7]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#08.2F09.2F2010 8]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#09.2F09.2F2010 9]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#10.2F09.2F2010 10]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#11.2F09.2F2010 11]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#12.2F09.2F2010 12]'''
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|- style="background:#f2f2f2; color:#78b41e"
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|'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#13.2F09.2F2010 13]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#14.2F09.2F2010 14]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#15.2F09.2F2010 15]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#16.2F09.2F2010 16]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#17.2F09.2F2010 17]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#18.2F09.2F2010 18]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#19.2F09.2F2010 19]'''
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|- style="background:#f2f2f2; color:#78b41e"
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|'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#20.2F09.2F2010 20]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#21.2F09.2F2010 21]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#22.2F09.2F2010 22]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#23.2F09.2F2010 23]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#24.2F09.2F2010 24]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#25.2F09.2F2010 25]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#26.2F09.2F2010 26]'''
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|- style="background:#f2f2f2; color:#78b41e"
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|'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#27.2F09.2F2010 27]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#28.2F09.2F2010 28]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#29.2F09.2F2010 29]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/miMeasure/September#30.2F30.2F2010 30]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/Homology_Based/August#31.2F08.2F2010 31]'''||colspan="5"|
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{| cellpadding="5" cellspacing="0" align="center" style="text-align: center; color:#f09600; border: 1.5px solid #333333;"
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|- border="0"
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! colspan="7" style="background:#78b41e;" | [http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October<font color="white">October</font>]
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|- style="background:#78b41e; color:white"
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|width="20pt"|'''M'''||width="20pt"|'''T'''||width="20pt"|'''W'''||width="20pt"|'''T'''||width="20pt"|'''F'''||width="20pt"|'''S'''||width="20pt"|'''S'''
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|- style="background:#f2f2f2; color:#78b41e"
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|colspan="4"| ||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#01.2F10.2F2010 1]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#02.2F10.2F2010 2]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#03.2F10.2F2010 3]'''
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|- style="background:#f2f2f2; color:#78b41e"
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|'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#04.2F10.2F2010 4]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#05.2F10.2F2010 5]'''
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|'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#06.2F10.2F2010 6]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#07.2F10.2F2010 7]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#08.2F10.2F2010 8]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#09.2F10.2F2010 9]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#10.2F10.2F2010 10]'''
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|- style="background:#f2f2f2; color:#78b41e"
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|'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#11.2F10.2F2010 11]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#12.2F10.2F2010 12]'''|'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#13.2F10.2F2010 13]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#14.2F10.2F2010 14]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#15.2F10.2F2010 15]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#16.2F10.2F2010 16]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#17.2F10.2F2010 17]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#18.2F10.2F2010 18]'''
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|- style="background:#f2f2f2; color:#78b41e"
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|'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#19.2F10.2F2010 19]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#20.2F10.2F2010 20]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#21.2F10.2F2010 21]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#22.2F10.2F2010 22]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#23.2F10.2F2010 23]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#24.2F10.2F2010 24]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#25.2F10.2F2010 25]'''
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|- style="background:#f2f2f2; color:#78b41e"
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|'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#26.2F10.2F2010 26]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#27.2F10.2F2010 27]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#28.2F10.2F2010 28]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#29.2F10.2F2010 29]'''||'''[http://2010.igem.org/Team:Heidelberg/Notebook/MiMeasure/October#22.2F30.2F2010 30]'''||colspan="3"|
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__NOTOC__
===13/09/2010===
===13/09/2010===
<br />
<br />
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DNA was stored in fridge afterwards
DNA was stored in fridge afterwards
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===14/09/2010===
===14/09/2010===
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Latest revision as of 02:01, 28 October 2010

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Example.jpg


 

13/09/2010


Restriction digest of psiCHECK-2 plasmid
This will be used as backbone for raPCR cloning. Enzymes: XhoI and NotI

Assay:

5 µL 10x NEBuffer 3
5 µL 10x BSA
5 µL plasmid (psiCHECK-2, ~370 ng/µL)
3 µL XhoI
1 µL NotI
18.6 µL H2O

Restriction digest was performed for approx. 5h

raPCR to create binding sites for different miRNAs This random assembly PCR (raPCR) will be done to create binding site patterns for the miRNAs mentioned. In the first PCR step the oligos will basically anneal and constructs of different lengths will form. In the second step, the stop oligos are used as primers to amplify the previously formed constructs.

  • first tries are: hsa-mir-122, hsa-mir122(ran9-12) and mm-mir-376a/375 (Oligos: ra001-003 and ra006)

stop-oligos: raPCR_AS13-stop_rev_NotI and raPCR_AS13-stop_fw_XhoI (ra017/018)
spacer: raPCR_AS13-spacer(0) and raPCR_AS13-spacer(10) (ra012/013)

Oligos were used in standard conc. (100µM)

  • 1. PCR
Oligo mir-122 mir-122(ran9-12) mir-375/376a
miR 1 or 3 µL 1 or 3 µL 0.5 or 1.5 µL (each)
spacer(0)or (10) 1 µL 1 µL 1 µL
stop 0 or 0.5 µL each 0 or 0.5 µL each 0 or 0.5 µL each


Total: 12 reactions
each reaction was set up in 30 µL, using 2x Phusion Mastermix for 12 cycles

Temp Time
95°05:00
95°00:30x 12 cycles
57°00:45
72°00:45
forever
  • PCR purification: each PCR was purified using Qiagen PCR purification Kit and eluted in 32 µL

for the next PCR, three assay will tried:

  1. 5µL eluate + 1 µL of each stop oligo in 50µL total volume
  2. 5µL eluate + 2 µL of each stop oligo in 50µL total volume
  3. 20µL eluate + 1 µL of each stop oligo in 50µL total volume

stop-oligos: raPCR_AS13-stop_rev_NotI and raPCR_AS13-stop_fw_XhoI

  • 2. PCR

In total there were 72 reactions. Each was run with 2x Phusion Mastermix, missing volume was filled with water.

Temp Time
95°05:00
95°00:30x 25 cycles
65°00:45
72°00:50
72°05:00
forever

DNA was stored in fridge afterwards

14/09/2010

72 PCRs were analyesed on 1% agarose gel

Best looking lanes of spacer(0) and spacer(10) were choosen for preparative gel

preparative gel (1.5%) was made for miR122

Sample for small Binding site patterns (100-250 bp) and large patterns (250-400 bp) were taken.

each were eluted in 1 column (a lot of work for gel extraction...)


15/09/2010

Gel extracted samples were digested with Not/Xho for cloning into psiCheck-2 vector: 5µL template in total 30µL using 1µL xho and 0.6µL Not enzyme

digest was then purified using qiagen nucleotide removal kit, elution in 30µL

due to a problem of the vector-size (it has 8000 instead of 6000 bp), ligation was set-up overnight at roomtemperature

ligation: 2µL buffer 1µL ligase 7µL water 1µL backbone (6000bp) 9µL restriction digest



16/09/2010

Transformation of ligations: 5µL ligation assay in 50µL TOP10 E.coli 25 min on ice 45sec heat shock on 42°C 1.5-2h shaking at 37°C

plated 200µL on Amp-Plates

after incubating ~8h, at 37°C, the plates were incubated overnight at room temperature

17/09/2010

Colonies were visible in reasonable numbers on every plate

colony pcr was performed to check clones

20µL assay PCR assay, using 2x PCR master mix (Taq) from Fermentas

one colony was dissolved in 20µL water

5µL of this bacteria solution was used as PCR template

PCR conditions as recommended from Fermentas

Minipreps will be setup in the evening for overnight cultures (4mL, Amp)

5 for each construct

28/09/2010

  • send 1.3, 1.5, 1.7, 3.8, 3.2 for sequencing


29/09/2010

  • got sequencing results of 1.3, 1.5, 1.7, 2.8, 3.2.
  • 1.3 - 3x - all ok
  • 1.5 - 2x - both ok
  • 1.7 - 3x - all ok
  • 2.8 - not ok
  • 3.7 - 2x - both ok seperated by 10 nucleotide spacer


30/09/2010

  • raPCRfrom above(1, 2, 3, 4)
  • PCR purification ( nanodrop: c ≈ 100ng/µl)
  • digested: 2 x 1 µg DNA:
  • EcoRI
  • PstI
  • gel purification (nanodrop: c ≈ 25ng/µl)
  • Ligation (Quick Ligase and overnight ligation with T4 ligase) into pSB1C3
  • Vector ≈ 2000 bp
  • Insert ≈ 200 bp
  • Transformation