Kun:LabNotes/Haplotyping/2010-8-26: Difference between revisions
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m (Created page with '==Illumina multiplex library construction== *Received sheared DNA from Sara. *End-repair: Fragmented DNA 85 μl NEBNext End Repair Reaction B…') |
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Incubate in a thermal cycler for 30 minutes at 37°C. | Incubate in a thermal cycler for 30 minutes at 37°C. | ||
Purified with AMPure beads. | Purified with AMPure beads. | ||
Conc(ng/ul) | |||
1A 17.7 | |||
1F 11.8 | |||
1G 7.3 | |||
2E 3.1 | |||
2F 5.1 | |||
*Ligation: | *Ligation: | ||
End Repaired, Blunt or dA-Tailed DNA | End Repaired, Blunt or dA-Tailed DNA 25 μl | ||
Quick Ligation Reaction Buffer (5X) 8 μl | Quick Ligation Reaction Buffer (5X) 8 μl | ||
20 μM DNA Adaptors | 20 μM DNA Adaptors 2 μl | ||
Quick T4 DNA Ligase 2.5 μl | Quick T4 DNA Ligase 2.5 μl | ||
H2O 2.5 μl | |||
Incubate in a thermal cycler for 15 minutes at 20°C. | Incubate in a thermal cycler for 15 minutes at 20°C. | ||
Purified with AMPure beads. | Purified with AMPure beads. | ||
Line 34: | Line 41: | ||
100 μl | 100 μl | ||
Barcodes 200bp | Barcodes 200bp | ||
1A | 1A Ind10 | ||
1F | 1F Ind11 | ||
1G | 1G Ind12 | ||
98C 15s ->(98C,5s -> 65C,20s -> 72C,15s)x15 -> 72C 2min. | 98C 15s ->(98C,5s -> 65C,20s -> 72C,15s)x15 -> 72C 2min. | ||
Terminated the reactions before the curves reach the plateau stage. | Terminated the reactions before the curves reach the plateau stage. | ||
*The libraries were not good. See [[Kun:LabNotes/GenomeSeq/2010-8-26]] | |||
*Repeated the library construction, and was able to make three good libraries: [[Kun:LabNotes/GenomeSeq/2010-9-10]] | |||
*Obtained two lanes of SE 60bp reads from HL072 run. | |||
Data file # reads | |||
GM20431_chr_1A_sequence.txt 7,613,296 | |||
GM20431_chr_1F_sequence.txt 7,760,883 | |||
GM20431_chr_1G_sequence.txt 6,546,229 |
Latest revision as of 00:57, 18 September 2010
Illumina multiplex library construction[edit]
- Received sheared DNA from Sara.
- End-repair:
Fragmented DNA 85 μl NEBNext End Repair Reaction Buffer (10X) 10 μl NEBNext End Repair Enzyme Mix 5 μl ----- 100 μl Incubate in a thermal cycler for 30 minutes at 20°C. Purified with AMPure beads.
- A-Tailing:
Blunt DNA 42 μl NEBNext dA-Tailing Reaction Buffer (10X) 5 μl Klenow Fragment (3´→ 5´ exo–) 3 μl ----- 50 μl Incubate in a thermal cycler for 30 minutes at 37°C. Purified with AMPure beads. Conc(ng/ul) 1A 17.7 1F 11.8 1G 7.3 2E 3.1 2F 5.1
- Ligation:
End Repaired, Blunt or dA-Tailed DNA 25 μl Quick Ligation Reaction Buffer (5X) 8 μl 20 μM DNA Adaptors 2 μl Quick T4 DNA Ligase 2.5 μl H2O 2.5 μl Incubate in a thermal cycler for 15 minutes at 20°C. Purified with AMPure beads.
- PCR:
Adapter ligased DNA 10 μl PCR_F(10uM) 2 μl PCR_R.N2IndX(10uM) 2 μl 50X SYBR Green I 0.8 μl H2O 37 μl 2X Phusion HF MM 50 μl ----- 100 μl Barcodes 200bp 1A Ind10 1F Ind11 1G Ind12 98C 15s ->(98C,5s -> 65C,20s -> 72C,15s)x15 -> 72C 2min. Terminated the reactions before the curves reach the plateau stage.
- The libraries were not good. See Kun:LabNotes/GenomeSeq/2010-8-26
- Repeated the library construction, and was able to make three good libraries: Kun:LabNotes/GenomeSeq/2010-9-10
- Obtained two lanes of SE 60bp reads from HL072 run.
Data file # reads GM20431_chr_1A_sequence.txt 7,613,296 GM20431_chr_1F_sequence.txt 7,760,883 GM20431_chr_1G_sequence.txt 6,546,229