Sam:LabNotes/Microbiome-new/2010-11-15: Difference between revisions

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>Sam Chiang
>Sam Chiang
 
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  [[File:sam111510-TBE PAGE.jpg|400px]]  [[File:sam111510-TBE PAGE-post cut.jpg|450px]]
  [[File:sam111510-TBE PAGE.jpg|400px]]  [[File:sam111510-TBE PAGE-post cut.jpg|450px]]


*Sine the estimated DNA amount in pooled lib is quite low (around 20x8=160ng => 160/2 = 80ng per well), I add 3.2uL tRNA(96ng/uL) to make the total nucleotide to 400ng before DNA recovery from gel-slice.
*Since the estimated DNA amount in pooled lib is quite low (around 20x8=160ng => 160/2 = 80ng per well), I add 3.2uL tRNA(96ng/uL) to make the total nucleotide to 400ng before DNA recovery from gel-slice.
*Shred the gel slice using pole-punctured 0.5mL non-sticky tubes. Centrifuge at 14,000rpm for 3min.  
*Shred the gel slice using pole-punctured 0.5mL non-sticky tubes. Centrifuge at 14,000rpm for 3min.  
*Incubate the gel slice mixture with '''500uL clean 1X TE at 37C for 2hr''' on the vortexer.
*Incubate the gel slice mixture with '''500uL clean 1X TE at 37C for 2hr''' on the vortexer.
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  [[File:sam111510-TBE PAGE -semi-quant.jpg|300px]]
  [[File:sam111510-TBE PAGE -semi-quant.jpg|300px]]
*The size selected libaray is confirmed around 300~400bp.
*The size selected libaray is confirmed around 300~400bp.
*The estimated concentration of 2nd size-selected lib. is '''~1.76 ng/uL'''. The total yield of library is 1.76*30= 52.8 ng
*The estimated concentration of 2nd size-selected lib. is '''~1.76 ng/uL'''(by PAGE gel semi-quantification). The total yield of library is 1.76*30= 52.8 ng
**Starting DNA amount: 20ng*8=160ng. Since I only size selected the partial region(~1/3 of whole smear), actually the DNA recovery rate is pretty high in the current experiment.
*The library is ready for cloning Sanger sequencing validation.
*The library is ready for cloning Sanger sequencing validation.
===Follow up: AMpure bead purification (11-19-'10)===
*The library pass the Sanger sequencing validation. 14/16 sequences results showed E.coli positive.
**http://genome-tech.ucsd.edu/LabNotes/index.php/Sam:LabNotes/Microbiome-new/2010-11-16_exp1
*Since the library still carry short(~50bp) fragments (shown on PAGE), I did an additional AMpure bead purification to remove these short fragments:
**Starting amount is set up as 30uL, I use 1V of AMpure beads(30uL) to bind on library DNA.
**Wash with 200uL 70% EtOH twice, air dry 2min.
**Elute DNA in 20uL pre-warmed H2O.
*Library was submitted to Alan for sequencing. Library tag: '''HC-MDA-Ecoli-SAGs(Ind1to8)-Nov15'''

Latest revision as of 19:16, 29 April 2011

2nd size selection of pooled Illumina library(short and long amplified E.coli SAGs -3rd test 11-07-'10)[edit]

Background[edit]

Procedures[edit]

2nd size selection(300~400bp)[edit]

  • The pooled library is ~40uL. The pooled library was seperated into two tube (20uL/tube) for size-selection using 5-well TBE-PAGE.
    • Sample well: 10uL H2O + 10uL 6X loading dye + 20uL DNA sample
    • Ladder well: 30uL H2O + 10uL 6X loading dye + 0.5uL Low mass ladder/1kb plus ladder
  • Run at 200V for 30min. Long staining (15min with foil wrap protection).
  • Band size between 300~400bp was cut in both pooled lib samples.
    • The size-selected regions should be the same regions I used for semi-quantification by TBE-PAGE from 11-14-'10
File:Sam111510-TBE PAGE.jpg  File:Sam111510-TBE PAGE-post cut.jpg
  • Since the estimated DNA amount in pooled lib is quite low (around 20x8=160ng => 160/2 = 80ng per well), I add 3.2uL tRNA(96ng/uL) to make the total nucleotide to 400ng before DNA recovery from gel-slice.
  • Shred the gel slice using pole-punctured 0.5mL non-sticky tubes. Centrifuge at 14,000rpm for 3min.
  • Incubate the gel slice mixture with 500uL clean 1X TE at 37C for 2hr on the vortexer.
  • Pellet the gel suspension at 14,000rpm for 1.5min at RT.
  • Transfer the supernatant onto Nanosap filter. Centrifuge at 14,000rpm for 1.5min at RT.
    • NOTE: I got ~350uL supernatant from each of samples.
  • Transfer the filtrate into clean 1.5-mL non-sticky tubes.
  • EtOH precipitation: 2.5V EtOH, 0.1V 3M NaOAc, 1.5uL Glycoblue. Mix well by inverting and incubate at -80C for 25min or more.
  • Centrifuge at 10,000xg 4C for 25min. Wash pellet with 75% EtOH, centrifuge at 10,000xg 4C for 5min. Air dry 5min. Elute the pellet in 15uL H2O. Pool eluted DNA together from two samples => 15X2 = 30uL.

TBE-PAGE semi-quantification[edit]

  • Since the EtOH-precipitation purified DNA is not able to be quantified by Nanodrop directly. I decided to use TBE-PAGE for another quantication. Also I can validate the result of size-selected library.
File:Sam111510-TBE PAGE -semi-quant.jpg
  • The size selected libaray is confirmed around 300~400bp.
  • The estimated concentration of 2nd size-selected lib. is ~1.76 ng/uL(by PAGE gel semi-quantification). The total yield of library is 1.76*30= 52.8 ng
    • Starting DNA amount: 20ng*8=160ng. Since I only size selected the partial region(~1/3 of whole smear), actually the DNA recovery rate is pretty high in the current experiment.
  • The library is ready for cloning Sanger sequencing validation.

Follow up: AMpure bead purification (11-19-'10)[edit]

  • The library pass the Sanger sequencing validation. 14/16 sequences results showed E.coli positive.
  • Since the library still carry short(~50bp) fragments (shown on PAGE), I did an additional AMpure bead purification to remove these short fragments:
    • Starting amount is set up as 30uL, I use 1V of AMpure beads(30uL) to bind on library DNA.
    • Wash with 200uL 70% EtOH twice, air dry 2min.
    • Elute DNA in 20uL pre-warmed H2O.
  • Library was submitted to Alan for sequencing. Library tag: HC-MDA-Ecoli-SAGs(Ind1to8)-Nov15