Team:Kyoto/Material

From 2011.igem.org

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<table class="materials">
<table class="materials">
<tr>
<tr>
-
<th>Name</th><th>Genotype and/or Relevant Features</th><th>Source or Reference
+
<th>Name</th><th>Genotype and/or Relevant Features</th><!--<th>Source or Reference
-
</th></tr>
+
</th>--></tr>
<tr>
<tr>
-
<td>D.melanogaster(fly)</td><td>Oregon-R-C</td><td>DGRC[http://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM=105669]
+
<td>D.melanogaster(fly)</td><td>Oregon-RS</td><!--<td>DGRC[http://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM=105669]
-
</td></tr>
+
</td>--></tr>
</table>
</table>
 +
<br/>
 +
==Strains(E.Coli)==
==Strains(E.Coli)==
-
<table class="materials">
 
-
<tr>
 
-
<th>Name</th><th>Genotype and/or Relevant Features</th><th>Source or Reference
 
-
</th></tr>
 
-
<tr>
 
-
<td>JM109</td><td><i>end</i>A, <i>rec</i>A1, <i>gyr</i>A96,<i>thi</i>,<i>hsd</i>R17,(r<sub>κ</sub><sup>-</sup>,m<sub>κ</sub><sup>+</sup>),<i>rel</i>A1, <i>sup</i>E44,
 
-
λ<sup>-</sup>,&Delta;(<i>lac-pro</i>AB),[F',<i>tra</i>D36,<i>pro</i>AB,<i>lac</i>l<sup>q</sup><i>Z</i>&Delta;M15]
 
-
<td>Promega[http://www.promega.com/products/cloning-and-dna-markers/cloning-tools-and-competent-cells/bacterial-strains-and-competent-cells/bacterial-strain-jm109_de3_/]
 
-
</td></tr>
 
-
 
{| class="materials"
{| class="materials"
!Name||Genotype and/or Relevant Features||Source or Reference
!Name||Genotype and/or Relevant Features||Source or Reference
|-
|-
-
|TOP10||F-, ''mcr''A, &Delta;(''mrr''-''hsd''RMS-''mcr''BC), &phi;80''lac''Z&Delta;M15, &Delta;''lac''X74, ''nup''G, ''rec''A1, ''ara''D139, &Delta;(''ara''-''leu'')7697, ''gal''E15, ''gal''K16 ''rps''L(Str<sup>R</sup>), ''end''A1, &lambda;-||Invitrogen
+
| JM109
 +
| <i>end</i>A, <i>rec</i>A1, <i>gyr</i>A96,<i>thi</i>,<i>hsd</i>R17,(r<sub>κ</sub><sup>-</sup>,m<sub>κ</sub><sup>+</sup>),<i>rel</i>A1, <i>sup</i>E44,λ<sup>-</sup>,&Delta;(<i>lac-pro</i>AB),[F',<i>tra</i>D36,<i>pro</i>AB,<i>lac</i>l<sup>q</sup><i>Z</i>&Delta;M15]
 +
|Promega[http://www.promega.com/products/cloning-and-dna-markers/cloning-tools-and-competent-cells/bacterial-strains-and-competent-cells/bacterial-strain-jm109_de3_/]
|-
|-
-
|rowspan="2"|KRX||rowspan="2"|[F&prime;, ''tra''D36, &Delta;''omp''P, ''pro''A<sup>+</sup>B<sup>+</sup>, ''lac''I<sup>q</sup>, &Delta;(''lac''Z)M15] &Delta;''omp''T, ''end''A1, ''rec''A1, ''gyr''A96 (Nal<sup>r</sup>), ''thi''-1, ''hsd''R17 (r<sub>k</sub><sup>–</sup>, m<sub>k</sub><sup>+</sup>), e14– (McrA–), ''rel''A1, ''sup''E44, &Delta;(''lac''-''pro''AB), &Delta;(''rha''BAD)::T7 RNA polymerase.||Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University
+
| BW25113
 +
| ∆(araD-araB)567, ∆lacZ4787(::rrnB-3), lambda-, rph-1, ∆(rhaD-rhaB)568, hsdR514
 +
| E.coliwiki[http://ecoliwiki.net/colipedia/index.php/BW25113]
 +
|}
 +
<br/>
 +
We got BW25113 from NIG, National Institute of Genetics.
 +
<br/>
 +
 
 +
==Strains(Streptomyces)==
 +
{| class="materials"
 +
!Name||Genotype and/or Relevant Features||Source or Reference
|-
|-
-
|(Promega [http://www.promega.com/catalog/catalogproducts.aspx?categoryname=productleaf_1698])
+
| Streptomyces avermitilis
 +
| MA-4680,ATCC 31267,BCRC 12382
 +
|JCM Catalog[http://www.jcm.riken.jp/cgi-bin/jcm/jcm_keyword?AN=Streptomyces&BN=avermitilis&CN=&DN=]
|-
|-
-
|BL21(DE3)pLysS||F–, ''omp''T, ''hsd''S<sub>B</sub> (r<sub>B</sub><sup>–</sup>, m<sub>B</sub><sup>–</sup>), ''dcm'', ''gal'', &lambda;(DE3), pLysS, Cm<sup>r</sup>.||Promega [http://www.promega.com/catalog/catalogproducts.aspx?categoryname=productleaf_1005]
+
| Streptomyces albogriseolus
 +
| ATCC 23875, BCRC 12230
 +
|JCM Catalog[http://www.jcm.riken.jp/cgi-bin/jcm/jcm_keyword?AN=Streptomyces&BN=albogriseolus&CN=&DN=]
|}
|}
 +
<br/>
 +
We got these strains from JCM, Japan Collection of Microorganisms.
 +
<br/>
-
 
+
==Primers for PCR amplification==
-
==Primers==
+
{| class="materials"
{| class="materials"
!Date||Name||Sequence
!Date||Name||Sequence
Line 49: Line 59:
|07/28||&Delta;TMD1 Forward||cgcggcagatataatggcggt
|07/28||&Delta;TMD1 Forward||cgcggcagatataatggcggt
|-
|-
-
|07/28||&Delta;TMD1 Reverse||gtcatgtttttctggcatcttcatgtct
+
|08/11||&Delta;TMD1 Reverse||gtcatgtttttctggcatcttcatgtct
 +
|-
 +
|08/11||glnL Forward||tctagaggagactgctttatggcaac
 +
|-
 +
|08/11||glnL Reverse||actagtaggaactatcgtcatcgactac
 +
|-
 +
|08/11||glnG Forward||tctagaggtgacgtttatgcaacga
 +
|-
 +
|08/11||glnG Reverse||actagtacacacaagctgtgaatcactc
|-
|-
|08/19, 08/24||Sam7 Forward||ggttcattcgtgaccttctcgacttc
|08/19, 08/24||Sam7 Forward||ggttcattcgtgaccttctcgacttc
Line 62: Line 80:
|-
|-
|08/23, 08/24||Deletion of Upstream Reverse||ctctagaagcggccgcgaattcc
|08/23, 08/24||Deletion of Upstream Reverse||ctctagaagcggccgcgaattcc
 +
|-
 +
|08/23||c-glnL Forward||gctctagaggagactgctttatggcaac
 +
|-
 +
|08/23||c-glnL Reverse||ggactagtaggaactatcgtcatcgactac
 +
|-
 +
|08/23||c-glnG Forward||gctctagaggtgacgtttatgcaacga
 +
|-
 +
|08/23||c-glnG Reverse||ggactagtacacacaagctgtgaatcactc
 +
|-
 +
|08/26||gln-promoter1||cggaattcgcggccgcttctagagattgca
 +
|-
 +
|08/26||gln-promoter2r||gaatgttgcaccaatatagtgcttcaatggaaacattaagcaccatgttggtgcaatctctagaagcggc
 +
|-
 +
|08/26||gln-promoter3||gaatgttgcaccaatatagtgcttcaatggaaacattaagcaccatgttggtgcaatctctagaagcggc
 +
|-
 +
|08/26||gln-promoter4r||ggactagtaaaagcgaaatctgtgccaacttttaaattgcccctaaaaggcgttatcatgcgcacc
 +
|-
 +
|08/28||cc-glnL Forward||ggaattcgcggccgcttctagaggagactgctttatggcaac
 +
|-
 +
|08/28||cc-glnG Forward||ggaattcgcggccgcttctagaggtgacgtttatgcaacga
 +
|-
 +
|08/28||rpoN Forward||ggaattcgcggccgcttctagaggttctgaacatgaagcaa
 +
|-
 +
|08/28||rpoN Reverse||ggactagtatccttatcggttgggtca
 +
|-
 +
|08/31||rpoN-Pstl-m2||ggactagtagtagacgctgaccccgtag
 +
|-
 +
|09/06||rpoN-Pstl-m1||gcaagatgccaaatggttgatcaagagtc
 +
|-
 +
|09/12||ChiA1 Forward||ggaattcgcggccgcttctagagattggtctggaccagtttgta
 +
|-
 +
|09/12||ChiA1 Reverse||ggactagtacactgccagttccacctacc
 +
|-
 +
|09/12||serine proteae Forward||ggaattcgcggccgcttctagagcctttgtggaggaacgaaac
 +
|-
 +
|09/12||serine proteae Reverse||ggactagtagtagacgctgaccccgtag
|-
|-
|09/13, 09/22||Add J23105 Forward||CAGTCCTAGGTACTATGCTAGCtactagtagcggccgctgc
|09/13, 09/22||Add J23105 Forward||CAGTCCTAGGTACTATGCTAGCtactagtagcggccgctgc
Line 76: Line 130:
|-
|-
| - ||VF (<partinfo>G00101</partinfo>)||attaccgcctttgagtgagc
| - ||VF (<partinfo>G00101</partinfo>)||attaccgcctttgagtgagc
 +
|}
 +
<br/>
 +
==Primers for Real time PCR==
 +
{| class="materials"
 +
!Date||Name||Sequence
 +
|-
 +
|09/13||sigma54-f||TTGATCCGGTCGGTGTG
 +
|-
 +
|09/13||sigma54-r||AGTGCGGAAGTCGTGATTG
 +
|-
 +
|09/13||GAPDH-f||GGTGCGAAGAAAGTGGTTATG
 +
|-
 +
|09/13||GAPDH-r||TGGTGCAGGAAGCGTTG
 +
|-
 +
|09/13||GUS-f||GGCAACAAGCCGAAAGAAC
 +
|-
 +
|09/13||GUS-r||GGCAATACTCCACATCACCAC
 +
|-
 +
|09/13||TBP-f||CAATTCATCTCGACCATCACAC
 +
|-
 +
|09/13||TBP-r||AAATCCACCACCTCTTTGACC
 +
|-
 +
|09/13||PGK-f||TCAACAAAGGCGAGAAGAAAG
 +
|-
 +
|09/13||actin-f||ACGGTGTGGTTTACTCCTCTTC
 +
|-
 +
|09/13||PGK-r||GAACCGATTTCGTGCTTGATAC
 +
|-
 +
|09/23||GUS-f||ACAGCCAAAAGCCAGACAG
 +
|-
 +
|09/23||GUS-r||TGACGACCAAAGCCAGTAAAG
 +
|-
 +
|09/23||TBP-f||ACGGCTCATGGGATGTATG
 +
|-
 +
|09/23||TBP-r||ATCCCCAGTTTGATGGTTTG
 +
|-
 +
|09/23||glnL1-f||GAGATGGCTCCGATGGATAAC
 +
|-
 +
|09/23||glnL1-r||ACTAAATCACGGGCAGCAAC
 +
|-
 +
|09/23||glnL2-f||TGCTGCCCGTGATTTAGTG
 +
|-
 +
|09/23||glnL2-r||ATTCGAGTAGTGATGGGTCAGG
 +
|-
 +
|09/23||glnL3-f||GATACGCTGTTTTACCCGATG
 +
|-
 +
|09/23||glnL3-r||GATAGGCAGGTAAACCGAGAAC
 +
|-
 +
|09/23||glnG1-f||GGCGGTACATTATTCCTCGAC
 +
|-
 +
|09/23||glnG1-r||TCCGCACATCCACTTTCAC
 +
|-
 +
|09/23||glnG2-f||TCAGCGCCTATCAACAAGG
 +
|-
 +
|09/23||glnG2-r||TGCTGCTGTTCCTGGTAATG
 +
|-
 +
|09/23||glnG3-f||CAGATTAAACAGCGCCATCC
 +
|-
 +
|09/23||glnG3-r||CAAACGCCCCTTGTTGATAG
 +
|-
 +
|09/23||sigma54promoter-rpoN-f||actaGAGGTTCTGaacatgaagc
 +
|-
 +
|09/23||sigma54promoter-rpoN-r||attactctccagcgcctgc
 +
|-
 +
|09/23||rpoN-glnLG-f||tactagaGGAGACTGCTTTatggc
 +
|-
 +
|09/23||rpoN-glnLG-r||cgccaggttgtcatcgattaac
 +
|-
 +
|09/28||bolA-f||CGTTTTCTGAATCGTCATCG
 +
|-
 +
|09/28||bolA-f||CGTTTTCTGAATCGTCATCG
 +
|-
 +
|09/28||bolA-r||ACAGGGAGGAGAGGCAAAG
 +
|-
 +
|09/28||csiE1-f||GCTCCACCATCTGTCCTTTC
 +
|-
 +
|09/28||csiE1-r||GGCAATATCATCATCCACACC
 +
|-
 +
|09/28||csi2-r||ATTGTCTGTCCCGCTGATG
 +
|-
 +
|09/28||dps-f||GGGACCACTCAAGTTATCAACAG
 +
|-
 +
|09/28||dps-r||GGTCAGCCAGTTCTTTCAGG
 +
|-
|}
|}
----
----

Latest revision as of 00:29, 6 October 2011

Contents

Materials

Strain(Fruits Fly)

NameGenotype and/or Relevant Features
D.melanogaster(fly)Oregon-RS


Strains(E.Coli)

NameGenotype and/or Relevant FeaturesSource or Reference
JM109 endA, recA1, gyrA96,thi,hsdR17,(rκ-,mκ+),relA1, supE44,λ-,Δ(lac-proAB),[F',traD36,proAB,laclqZΔM15] Promega[http://www.promega.com/products/cloning-and-dna-markers/cloning-tools-and-competent-cells/bacterial-strains-and-competent-cells/bacterial-strain-jm109_de3_/]
BW25113 ∆(araD-araB)567, ∆lacZ4787(::rrnB-3), lambda-, rph-1, ∆(rhaD-rhaB)568, hsdR514 E.coliwiki[http://ecoliwiki.net/colipedia/index.php/BW25113]


We got BW25113 from NIG, National Institute of Genetics.

Strains(Streptomyces)

NameGenotype and/or Relevant FeaturesSource or Reference
Streptomyces avermitilis MA-4680,ATCC 31267,BCRC 12382 JCM Catalog[http://www.jcm.riken.jp/cgi-bin/jcm/jcm_keyword?AN=Streptomyces&BN=avermitilis&CN=&DN=]
Streptomyces albogriseolus ATCC 23875, BCRC 12230 JCM Catalog[http://www.jcm.riken.jp/cgi-bin/jcm/jcm_keyword?AN=Streptomyces&BN=albogriseolus&CN=&DN=]


We got these strains from JCM, Japan Collection of Microorganisms.

Primers for PCR amplification

DateNameSequence
07/21S Forward (Same as SRRz Forward)gGAATTCGCGGCCGCTTCTAGAGgcctggatttgttctatcagtaatcga
07/21S ReverseCTGCAGCGGCCGCTACTAGTAttattgatttctaccatcttctactccggc
07/21SRRz ReverseCTGCAGCGGCCGCTACTAGTAtgagttgcccatcgatatgggc
07/28ΔTMD1 Forwardcgcggcagatataatggcggt
08/11ΔTMD1 Reversegtcatgtttttctggcatcttcatgtct
08/11glnL Forwardtctagaggagactgctttatggcaac
08/11glnL Reverseactagtaggaactatcgtcatcgactac
08/11glnG Forwardtctagaggtgacgtttatgcaacga
08/11glnG Reverseactagtacacacaagctgtgaatcactc
08/19, 08/24Sam7 Forwardggttcattcgtgaccttctcgacttc
08/19, 08/24Sam7 Reverseaggcgataatggcgcacatc
08/20SRRz Forward RetrygGAATTCGCGGCCGCTTCTAGAGgagcaaatccccttattgggggtaagacatg
08/20SRRz Reverse RetryCTGCAGCGGCCGCTACTAGTAgcaactctatctgcactgctcattaatatacttctgg
08/23, 08/24Deletion of Upstream Forwardgagcaaatccccttattgggggtaagacatg
08/23, 08/24Deletion of Upstream Reversectctagaagcggccgcgaattcc
08/23c-glnL Forwardgctctagaggagactgctttatggcaac
08/23c-glnL Reverseggactagtaggaactatcgtcatcgactac
08/23c-glnG Forwardgctctagaggtgacgtttatgcaacga
08/23c-glnG Reverseggactagtacacacaagctgtgaatcactc
08/26gln-promoter1cggaattcgcggccgcttctagagattgca
08/26gln-promoter2rgaatgttgcaccaatatagtgcttcaatggaaacattaagcaccatgttggtgcaatctctagaagcggc
08/26gln-promoter3gaatgttgcaccaatatagtgcttcaatggaaacattaagcaccatgttggtgcaatctctagaagcggc
08/26gln-promoter4rggactagtaaaagcgaaatctgtgccaacttttaaattgcccctaaaaggcgttatcatgcgcacc
08/28cc-glnL Forwardggaattcgcggccgcttctagaggagactgctttatggcaac
08/28cc-glnG Forwardggaattcgcggccgcttctagaggtgacgtttatgcaacga
08/28rpoN Forwardggaattcgcggccgcttctagaggttctgaacatgaagcaa
08/28rpoN Reverseggactagtatccttatcggttgggtca
08/31rpoN-Pstl-m2ggactagtagtagacgctgaccccgtag
09/06rpoN-Pstl-m1gcaagatgccaaatggttgatcaagagtc
09/12ChiA1 Forwardggaattcgcggccgcttctagagattggtctggaccagtttgta
09/12ChiA1 Reverseggactagtacactgccagttccacctacc
09/12serine proteae Forwardggaattcgcggccgcttctagagcctttgtggaggaacgaaac
09/12serine proteae Reverseggactagtagtagacgctgaccccgtag
09/13, 09/22Add J23105 ForwardCAGTCCTAGGTACTATGCTAGCtactagtagcggccgctgc
09/13, 09/22Add J23105 ReverseAGCTAGCCGTAAActctagtatataaacgcagaaaggcccacc
10/10Deletion of GFP Forward (Primer1)ccaggcatcaaataaaacgaaaggctc
10/10Deletion of GFP-DT Forward (Primer2)tactagtagcggccgctgc
10/10Deletion of GFP, GFP-DT Reverse (Primer3)ctctagtattattgatttctaccatcttctactcc
- VF2 (<partinfo>G00100</partinfo>)tgccacctgacgtctaagaa
- VF (<partinfo>G00101</partinfo>)attaccgcctttgagtgagc


Primers for Real time PCR

DateNameSequence
09/13sigma54-fTTGATCCGGTCGGTGTG
09/13sigma54-rAGTGCGGAAGTCGTGATTG
09/13GAPDH-fGGTGCGAAGAAAGTGGTTATG
09/13GAPDH-rTGGTGCAGGAAGCGTTG
09/13GUS-fGGCAACAAGCCGAAAGAAC
09/13GUS-rGGCAATACTCCACATCACCAC
09/13TBP-fCAATTCATCTCGACCATCACAC
09/13TBP-rAAATCCACCACCTCTTTGACC
09/13PGK-fTCAACAAAGGCGAGAAGAAAG
09/13actin-fACGGTGTGGTTTACTCCTCTTC
09/13PGK-rGAACCGATTTCGTGCTTGATAC
09/23GUS-fACAGCCAAAAGCCAGACAG
09/23GUS-rTGACGACCAAAGCCAGTAAAG
09/23TBP-fACGGCTCATGGGATGTATG
09/23TBP-rATCCCCAGTTTGATGGTTTG
09/23glnL1-fGAGATGGCTCCGATGGATAAC
09/23glnL1-rACTAAATCACGGGCAGCAAC
09/23glnL2-fTGCTGCCCGTGATTTAGTG
09/23glnL2-rATTCGAGTAGTGATGGGTCAGG
09/23glnL3-fGATACGCTGTTTTACCCGATG
09/23glnL3-rGATAGGCAGGTAAACCGAGAAC
09/23glnG1-fGGCGGTACATTATTCCTCGAC
09/23glnG1-rTCCGCACATCCACTTTCAC
09/23glnG2-fTCAGCGCCTATCAACAAGG
09/23glnG2-rTGCTGCTGTTCCTGGTAATG
09/23glnG3-fCAGATTAAACAGCGCCATCC
09/23glnG3-rCAAACGCCCCTTGTTGATAG
09/23sigma54promoter-rpoN-factaGAGGTTCTGaacatgaagc
09/23sigma54promoter-rpoN-rattactctccagcgcctgc
09/23rpoN-glnLG-ftactagaGGAGACTGCTTTatggc
09/23rpoN-glnLG-rcgccaggttgtcatcgattaac
09/28bolA-fCGTTTTCTGAATCGTCATCG
09/28bolA-fCGTTTTCTGAATCGTCATCG
09/28bolA-rACAGGGAGGAGAGGCAAAG
09/28csiE1-fGCTCCACCATCTGTCCTTTC
09/28csiE1-rGGCAATATCATCATCCACACC
09/28csi2-rATTGTCTGTCCCGCTGATG
09/28dps-fGGGACCACTCAAGTTATCAACAG
09/28dps-rGGTCAGCCAGTTCTTTCAGG
Retrieved from "http://2011.igem.org/Team:Kyoto/Material"