Sam:LabNotes/Microbiome-new/2010-1-28: Difference between revisions
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>Sam Chiang |
>Sam Chiang |
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(4 intermediate revisions by the same user not shown) | |||
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='''16S LD-PCR 40cycle amplification for | ='''16S LD-PCR 40cycle amplification for bacteria genotyping'''= | ||
==Backgorund== | ==Backgorund== | ||
Line 7: | Line 7: | ||
==Procedure== | ==Procedure== | ||
Taq-Gold(ABI) recipe | Taq-Gold(ABI) recipe | ||
1rxn 4+1rxn | |||
----------------------------------------- | --------------------------------------------- | ||
H2O | H2O 13.5 67.5 | ||
10X buf | 10X buf 2.0 10.0 | ||
MgCl2 | MgCl2 2.0 10.0 | ||
Micro Seq primer(f+r,10uM) 1.0 5.0 - Microseq_16S | |||
dNTP(10mM) | dNTP(10mM) 0.4 2.0 | ||
Taq-Gold Enzyme | Taq-Gold Enzyme 0.1 0.5 | ||
-------------------------------------- | --------------------------------------------- | ||
19.0 95.0 95/5=19 template-1uL | |||
'''Template (1uL): 11-1, 11-2, 12-1, 12-2''' | '''Template (1uL): 11-1, 11-2, 12-1, 12-2''' | ||
11-1, 12-1: 1uL eliqote from 20uL size selected 1st PCR amplicons | 11-1, 12-1: 1uL eliqote from 20uL (E-gel) size selected 1st PCR amplicons | ||
11-2, 12-2: 1uL eliqote from 1st PCR amplicons | 11-2, 12-2: 1uL eliqote from 1st PCR amplicons | ||
Line 37: | Line 37: | ||
==Sequence results== | ==Sequence results== | ||
*I got very high quality scores (49 and 50) for both samples. | *I got very high quality scores (49 and 50) for both samples. | ||
*'''For both sequence, the blast (NCBI nt database) results hit | *'''For both sequence, the blast (NCBI nt database) results hit unculturable bacterium''' | ||
Sequence File : 11-1-sam012810-16S.seq | Sequence File : 11-1-sam012810-16S.seq |
Latest revision as of 18:50, 25 May 2010
16S LD-PCR 40cycle amplification for bacteria genotyping[edit]
Backgorund[edit]
- I identified two possible positive amplicons by 16S-LD PCR validation. However the PCR products concentration might be too low for sequencing.
- By doing Size selection + 2nd PCR amplification, I can get enough specific PCR product for sequencing.
Procedure[edit]
Taq-Gold(ABI) recipe 1rxn 4+1rxn --------------------------------------------- H2O 13.5 67.5 10X buf 2.0 10.0 MgCl2 2.0 10.0 Micro Seq primer(f+r,10uM) 1.0 5.0 - Microseq_16S dNTP(10mM) 0.4 2.0 Taq-Gold Enzyme 0.1 0.5 --------------------------------------------- 19.0 95.0 95/5=19 template-1uL Template (1uL): 11-1, 11-2, 12-1, 12-2 11-1, 12-1: 1uL eliqote from 20uL (E-gel) size selected 1st PCR amplicons 11-2, 12-2: 1uL eliqote from 1st PCR amplicons Program "16S-amp (40cycle)
Results[edit]
- 1uL 2nd-PCR amplicons were varified by 2% agarose gel
- Sample well: 1uL sample + 5uL 0.5X TBE + 2uL 6X loading dye
- Ladder: 5uL pre-diluted 1kb-plus ladder
File:Sam012810-2nd PCR.jpg
- The E-gel size selected templates (11-1 and 12-1) showed higer specificity than direct-eliqote template from 1st PCR amplicons (11-2, 12-2)
- I only use 2nd PCR amplcons from 11-1 and 12-1 for Sanger sequencing.
- I purifified the 2nd PCR product(20uL) with Montage filter and sent to Genewiz for sequecing.
Sequence results[edit]
- I got very high quality scores (49 and 50) for both samples.
- For both sequence, the blast (NCBI nt database) results hit unculturable bacterium
Sequence File : 11-1-sam012810-16S.seq >11-1-sam012810-16S_A09.ab1 CNNNNANNNNNGNCGNGGNATGATGCNATTTGAACGGACCTTTTTTGNAATAACCCTTCTGGTGGAAATTAGGAAAGGTT AGTGGCAGACGGGGGAGTAACGCGTAGAAAATCTACCTTAAAGACTGGGACAACAGTTGGAAACGACTGCTAATACCGGA TACGCTGCACATAGGGCATCCTAGGTGCAGGAAAAGAGGCCTCTTAACAATGCTCCTGCTTTTAGATGAGTCTGCGTCTG ATTAGCTAGATGGTGGGGTAACGGCTTACCATGGCGACGATCAGTAGTCGGCCTGAGAGGGTGACCGGCCACATTGGGAC TGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTGGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCG CGTGATCGAATGAAGGCCTTCGGGTTGTAAAGATCTGTTGACAGGGACGAATAAGCAATGCGAATAGTTTTGTGTATGAC GGTACCTGTTTAGAAAGCTCCGGCTAACTACGTGCCAGCAGCCGCGGTAA Sequence File : 12-1-sam012810-16S.seq >12-1-sam012810-16S_B09.ab1 CNNNNANNNNGGCGNNGTATGATGCTATTTGAGGGGCATCAACTTATGGTGGCTGGGGCTGGTGACCGGACGACGTTTGC GGAAACCGTACGNACCTTCCTTGGTAAGGGGGATAGCCCATAGAAATGTGGATTAATACCCCGTAAGATAGTGGGATGGC ATCATACTACTATTATAGTTACGACGCTTGAAGATGGGTGTGCGTCTGATTAGGTAGTTGGCGGGGTAAAGGCCCACCAA GCCTTCGATCAGTAGCTGATGTGAGAGCATGATCAGCCACACGGGCACTGAGACACGGGCCCGACTCCTACGGGAGGCAG CAGTAAGGAATATTGGTCAATGGACGCAAGTCTGAACCAGCCATGCCGCGTGAAGGATGAAGGTCCTCTGGATTGTAAAC TTCTTTTATAGGGGGCGAAAAAAGGGAAATCTTTCTCACTTGACAGTACCCTATGAATAAGCACCGGCTAACTCCGTGCC AGCAGCCGCGGTAA