Brandon:LabNotes/Project1/2015-6-10

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tn5-059 NXTA_ME_B for secondary fragmentation trial with cell samples, with ez-tn5 nxta_me_B control, Round 2[edit]


  • will test with 1000 cell john chang samples to make sure they work. when preparing 100 cell, 500 cell GM12878 libraries used custom transposons with ez-tn5 for secondary fragmentation and adaptor addition. tn5059 should be better.



AFTER IVT RNA HAS ALREADY BEEN GENERATED AND CLEANED WITH ZYMO


  • sample list
1. idx49, 2015-5-26, 8. t7-top2, 5X tn5-059, 200 cells, A2, ez-tn5
2. idx50, 2015-5-26, 8. t7-top2, 5X tn5-059, 200 cells, A2, tn5-059
3. idx51, 2015-5-26, 9. t7-top2, 5X tn5-059, 1000 cells, N1, ez-tn5
4. idx52, 2015-5-26, 9. t7-top2, 5X tn5-059, 1000 cells, N1, tn5-059
5. idx53, 2015-5-26, 9. t7-top2, 5X tn5-059, 1000 cells, N1, tn5-059
6. idx54, 2015-5-26, 11. t7-top2, 5X tn5-059, 1000 cells, A1, ez-tn5
7. idx55, 2015-5-26, 11. t7-top2, 5X tn5-059, 1000 cells, A1, tn5-059
8. idx56, 2015-5-26, 11. t7-top2, 5X tn5-059, 1000 cells, A1, tn5-059
9. idx57, 2015-5-26, 13. t7-top2, 5X tn5-059, 6 ng pure DNA, ez-tn5
10. idx58, 2015-5-26, 13. t7-top2, 5X tn5-059, 6 ng pure DNA, tn5-059
11. idx59, 2015-5-26, 14  t7-top2, 5X tn5-059, NTC, ez-tn5
12. idx60, 2015-5-26, 14  t7-top2, 5X tn5-059, NTC, tn5-059


  • Amounts of RNA and water to add for MMLV RT (50 ng RNA)
' ul for 50 ng ' N-H20
idx49, 2015-5-26, 8. t7-top2, 5X tn5-059, 200 cells, A2, ez-tn5 2.447892252 7.552107748
idx50, 2015-5-26, 8. t7-top2, 5X tn5-059, 200 cells, A2, tn5-059 2.447892252 7.552107748
idx51, 2015-5-26, 9. t7-top2, 5X tn5-059, 1000 cells, N1, ez-tn5 0.926128791 9.073871209
idx52, 2015-5-26, 9. t7-top2, 5X tn5-059, 1000 cells, N1, tn5-059 0.926128791 9.073871209
idx53, 2015-5-26, 9. t7-top2, 5X tn5-059, 1000 cells, N1, tn5-059 0.926128791 9.073871209
idx54, 2015-5-26, 11. t7-top2, 5X tn5-059, 1000 cells, A1, ez-tn5 0.764755128 9.235244872
idx55, 2015-5-26, 11. t7-top2, 5X tn5-059, 1000 cells, A1, tn5-059 0.764755128 9.235244872
idx56, 2015-5-26, 11. t7-top2, 5X tn5-059, 1000 cells, A1, tn5-059 0.764755128 9.235244872
idx57, 2015-5-26, 13. t7-top2, 5X tn5-059, 6 ng pure DNA, ez-tn5 0.724059485 /8 9.275940515
idx58, 2015-5-26, 13. t7-top2, 5X tn5-059, 6 ng pure DNA, tn5-059 0.724059485 /8 9.275940515
idx59, 2015-5-26, 14 t7-top2, 5X tn5-059, NTC, 1 9
idx60, 2015-5-26, 14 t7-top2, 5X tn5-059, NTC, 1 9


8. single strand synthesis MMLV RT (Clontech)

20 uL reaction

1. Add 2.5 uL 20 uM (100 ng total) RANDOM HEXAMERS to RNA sample. Bring to final volume of 12.5 uL with
   Nuclease free H2O

2. heat the mixture to 70C fo 3 minutes.  Immediately cool on ice.

3. Add the following to the reaction.
   2  uL 5X first strand buffer
   2  uL dNTP mix
   2  uL 100 mM DTT
   1  uL N-H20
  .5 uL SMART MMLV RT and mix (ADD LAST!!!!!)
  ____
   20 uL total

4. Incuvate first at Room Temperature for 10 minutes. Then incubate at 42C for 60 minutes.

5. Terminate the reaction by heating at 70C for 10 minutes



9. RNase H digestion

  • Use .5 Units for 20 uL reaction. Stock is at 5 Units/ul, thus dilute 10X and use 1 uL per reaction.

a. Add 1 uL of 10X diluted Rnase H to the reaction.

b. Incubate for 20 minutes at 37C.


'SAMPLES 5,8 GET NO SSS_NPA_PRMR, GET WATER INSTEAD'FORGOT TO NOT ADD SSS_NPA_PRMR

10. Second strand synthesis: Adding sss_NPA_prmr primer and polymerases. Can incubate at higher temps (usually at 16C since RNA is nicked) since sss_NPA_prmr has a high Tm.

a. Add 2.5 uL of 20 uM sss_NPA_prmr to each reaction. 

b. Incubate solutions for 2 minutes at 65C. Cool immediately on ice.


d. Add polymerases etc to reactions

          taq5X: Add  5.875 uL, Incubate at 72C for 8 minutes


11. Clean DNA with AMPURE beads depending. elute in 20 uL and concentreate. (can also use qiaquick)

  • USED AMPURE DNA BEADS AT 1:1.8X RATIO
  • add 45 uL N-H2O
  • add 135 uL beads per reaction
  • elute on 20 uL

can quantitate with Qubit or on TBU gel.


11.5. Eluted DNA into 20 uL per sample, since when eluting in smaller amounts more sample is lost. Thus after elution used vaccum centrifuge commentator to concentrate sample size to ~4-5 uL per sample.

  • Also ~4-5 uL per sample is preferred for transposition, which has always been performed in low volume solutions. Additionally less transposome will be needed when doing that.

RAN FOR 16 MINUTES


12. Fragmenting and 3' End tagging with Custom Nextera transposome

USING NXTA_ME_B WITH TN5059, SAMPLES 2,4,5,7,8,10,12

EZ-TN5 NXTA_ME_B FOR CONTROL, SAMPLES 1,3,6,9,11

1 uL custom buffer D6
2 uL lysed/pure genomic DNA (X ng/pg DNA)
X uL Nuclease free H2O
1 uL prepared T7 transposomes (MAKE SURE TO ADD LAST)
___________
5 uL total solution

Incubate at 55C for 6 minutes, cool briefly on ice after


13. Protease digestion of transposase, protease inactivation

To each tube, add:
1 uL  Qiagen Protease, for 5 uL reaction 1 uL of .5 for .1 AU final. (stock is 5 AU and diluted 10X. want .5 AU/uL final [])
Incubate: 50C 10 minutes, 70C 20 minutes



14. Fill in reaction

  • Add 6 uL 2X taq polymerase, run at 72C for 3 minutes. (same as nextera)


15. PCR addition of barcodes MAKE SURE TO USE NEXTERA INDEXES!!!!!

KAPA SYBR FAST qPCR mix until saturation, X35 cycles
sample list
1. idx49, 2015-5-26, 8. t7-top2, 5X tn5-059, 200 cells, A2, ez-tn5
2. idx50, 2015-5-26, 8. t7-top2, 5X tn5-059, 200 cells, A2, tn5-059
3. idx51, 2015-5-26, 9. t7-top2, 5X tn5-059, 1000 cells, N1, ez-tn5
4. idx52, 2015-5-26, 9. t7-top2, 5X tn5-059, 1000 cells, N1, tn5-059
5. idx53, 2015-5-26, 9. t7-top2, 5X tn5-059, 1000 cells, N1, tn5-059
6. idx54, 2015-5-26, 11. t7-top2, 5X tn5-059, 1000 cells, A1, ez-tn5
7. idx55, 2015-5-26, 11. t7-top2, 5X tn5-059, 1000 cells, A1, tn5-059
8. idx56, 2015-5-26, 11. t7-top2, 5X tn5-059, 1000 cells, A1, tn5-059
9. idx57, 2015-5-26, 13. t7-top2, 5X tn5-059, 6 ng pure DNA, ez-tn5
10. idx58, 2015-5-26, 13. t7-top2, 5X tn5-059, 6 ng pure DNA, tn5-059
11. idx59, 2015-5-26, 14.  t7-top2, 5X tn5-059, NTC, ez-tn5
12. idx60, 2015-5-26, 14.  t7-top2, 5X tn5-059, NTC, tn5-059
9  uL Taq2X
2  uL primers, 2 uL F, (T7-top2-PCR-iaf, OR iaf2, iaf3) USED iaf2
2  uL NXTA indexes PCR_R.NXTAInd[XX], SPECIFIC TO EACH SAMPLE
4  uL H2O
1  uL 25X SYBR green
12 uL DNA template
_____________
30 uL

KAPA SYBR cycles:
72C 3 m, 95C 30s, (95C for 10s, 63C for 30s, 72C for 1 min) X15, 72C for 3 min, 4C forever

  • terminate before curves saturate (usually cycle 6-8)


16. Gel Size selection

  • gel size select from 400-800 bp, follow gel size selection protocol
  • do not need to include controls.



Results[edit]

  • PCR addition of barcodes
  • ez-tn5 PCR curves are normal when compared to previous runs with it. tn5-059 just goes alot higher

File:2015-06-10 nxta me b 059 eztn5, cells testing.bmp


  • gel after PCR addition of barcodes

File:ZhangLab 2 2015-06-10 22hr 15min-labeled.jpg File:ZhangLab 2 2015-06-10 22hr 18min-labeled.jpg


  • amounts for gel size selection
6/11/2015 gel size selection, nxta_me_b, 059 v ez-tn5 ' ' ' ' ' ' '
for 50 ng
1. idx49, 2015-5-26, 8. t7-top2, 5X tn5-059, 200 cells, A2, ez-tn5 10679.48032 9.661248207 8.280503543
2. idx50, 2015-5-26, 8. t7-top2, 5X tn5-059, 200 cells, A2, tn5-059 31953.25095 34.1974497 2.339355733
3. idx51, 2015-5-26, 9. t7-top2, 5X tn5-059, 1000 cells, N1, ez-tn5 8970.490267 7.690176648 10.40288197
4. idx52, 2015-5-26, 9. t7-top2, 5X tn5-059, 1000 cells, N1, tn5-059 24932.33074 26.09983899 3.065153008
5. idx53, 2015-5-26, 9. t7-top2, 5X tn5-059, 1000 cells, N1, tn5-059, no sss_NPA 24637.73073 25.76006071 3.105582743 80
6. idx54, 2015-5-26, 11. t7-top2, 5X tn5-059, 1000 cells, A1, ez-tn5 7369.08022 5.843182982 13.69116802 10
7. idx55, 2015-5-26, 11. t7-top2, 5X tn5-059, 1000 cells, A1, tn5-059 24035.75072 25.06576428 3.191604258 800
8. idx56, 2015-5-26, 11. t7-top2, 5X tn5-059, 1000 cells, A1, tn5-059, no sss_NPA 19386.32058 19.70332258 4.060228911
9. idx57, 2015-5-26, 13. t7-top2, 5X tn5-059, 6 ng pure DNA, ez-tn5 12923.34039 7.323302629 10.92403306 0.8 total dye
10. idx58, 2015-5-26, 13. t7-top2, 5X tn5-059, 6 ng pure DNA, tn5-059 32584.23097 19.31676935 4.141479278 0.8 49.73647819 9.947295638
11. idx59, 2015-5-26, 14 t7-top2, 5X tn5-059, NTC, ez-tn5 602.1000179 0 #DIV/0!
12. idx60, 2015-5-26, 14 t7-top2, 5X tn5-059, NTC, tn5-059 474.6700141 0 #DIV/0!


  • gel size selection

File:ZhangLab 2 2015-06-11 12hr 53min-labeled.jpg


  • gel size selection validation

File:ZhangLab 2 2015-06-11 16hr 34min-labeled.jpg

future[edit]

  • for PCR curves, ez-tn5 PCR curves are normal when compared to previous runs with it. tn5-059 just goes alot higher. sequencing better work this time. did not mess up PCR like last time


  • however sequencing didnt work, thus ordering new reagents and enzymes. think it might be bad MMLV since have been using the same one for a couple years. also getting new random hexamers, have new sss_NPA_prmr.