Brandon:LabNotes/Project1/2015-9-29

From ZhangLabWiki
Jump to navigation Jump to search

Trying exo I AGAIN to remove sss_nXTv2_prmr and cleaning with DNA clean and concentrator[edit]

  • anneal at 59C instead of 63C
  • use KAPA sybr fast instead of taq5X
  • use 50 uL PCR reactions, fill in during PCR
  • will use 10% DMF final in reaction as that is what is used with pure DNA tagmentations normally.
  • using shorter i5/i7 primers since maybe that is cause the 250 bp band after PCR


  • trying scheme #3

File:2015-10-02 experiemnts summary.png


Protocol[edit]

AFTER IVT RNA HAS ALREADY BEEN GENERATED AND CLEANED WITH ZYMO


Samples:
1. 9/24/2015 RNA #1+2, i502_T7-1_short-i701_orig, T7-nXTv2_i5-1, 5X tn5059, 500 cells Rep1,2
2. 9/24/2015 RNA #3, i502_T7-1_short-i702_orig, T7-nXTv2_i5-1, 5X tn5059, 500 cells Rep3
3. 9/24/2015 RNA #5, i502_T7-1_short-i703_orig, T7-nXTv2_i5-1, 5X tn5059, 6 ng pure DNA
4. 9/24/2015 RNA #6, i503_T7-1_short-i701_orig, T7-nXTv2_i5-1, 5X tn5059, NTC


  • Amounts of RNA and water to add for MMLV RT (50 ng RNA)
9/25/2015 intensity ng/ul ' ' ' ' '
1540.165708 5
441.3047926 2.5 in 10 ul for 50 ng
1. i502_T7-1_long-i701_long, T7-nXTv2_i5-1, 5X tn5059, 500 cells Rep1 3737.306598 9.998678313 99.98678313 5.000660931
2. i502_T7-1_long-i702_long, T7-nXTv2_i5-1, 5X tn5059, 500 cells Rep2 3910.542279 10.3928039 103.928039 4.811021211
3. i502_T7-1_long-i703_long, T7-nXTv2_i5-1, 5X tn5059, 500 cells Rep3 10229.91571 24.76990419 247.6990419 2.01857866
4. i503_T7-1_long-i701_long, T7-nXTv2_i5-1, 5X tn5059, 500 cells Rep4 4889.326632 12.61961973 126.1961973 3.962084521
5. i503_T7-1_long-i702_long, T7-nXTv2_i5-1, 5X tn5059, 6 ng pure DNA 97614.73967 223.5776485 2235.776485 0.223635951 /4 55.89441214 0.894543803
6. i503_T7-1_long-i703_long, T7-nXTv2_i5-1, 5X tn5059, NTC 257.4794671 2.081782092 20.81782092 1 uL
0 1.495994883 14.95994883 0
-83.77946196 1.305389637 13.05389637 38.30274009
#DIV/0!

11. single strand synthesis MMLV RT (Clontech)


a. Add 2.5 uL 20 uM (100 ng total) RANDOM HEXAMERS to RNA sample. Bring to final volume of 11.5 uL with
   Nuclease free H2O

b. heat the mixture to 70C for 3 minutes. Immediately cool on ice.

c. Add the following to the reaction.
   4  uL 5X first strand buffer
   2  uL dNTP mix
   2  uL 100 mM DTT
  .5 uL SMART MMLV RT and mix (ADD LAST!!!!!)
  ___________________________
   20 uL total

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

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


12. 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.


13. Second strand synthesis: Adding sss_nXTv2 primer and polymerases. Can incubate at higher temps (usually at 16C since RNA is nicked) since sss_nXTv2 has a high Tm.

a. Add 2.5 uL of 20 uM sss_nXTv2 to each reaction.

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

c. Add 5.875 uL taq5X to reactions, Incubate at 72C for 8 minutes


14. Exo I treatment, 3 uL (1 uL per 10 uL of reaction (20 units/uL), incubate 37C for 20 minutes


15. Clean with Zymo DNA clean and concentrator, 5 volumes DNA binding solution, elute 6 uL


16. Fragmenting and 3' End tagging with [1X] custom nXTv2_i7 Tn5059 transposome and custom tagmentation buffer D6

2 uL custom tagmentation buffer USED 50% DMF, 10% FINAL IN REACTION
X uL cDNA sample
X uL Nuclase free H2O
2 uL prepared 1X T7 transposomes (MAKE SURE TO ADD LAST)
___________
10 uL total solution

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


17. Protease digestion of transposase, protease inactivation

To each tube, add:
2 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



18. PCR addition of barcodes USING NEXTERA XT V2 modified i5 (T7-1_S5XX) AND i7 (N7XX) SEQUENCES!!!!!

Samples:
1. 9/24/2015 RNA #1+2, i502_T7-1_short-i701_orig, T7-nXTv2_i5-1, 5X tn5059, 500 cells Rep1,2
2. 9/24/2015 RNA #3, i502_T7-1_short-i702_orig, T7-nXTv2_i5-1, 5X tn5059, 500 cells Rep3
3. 9/24/2015 RNA #5, i502_T7-1_short-i703_orig, T7-nXTv2_i5-1, 5X tn5059, 6 ng pure DNA
4. 9/24/2015 RNA #6, i503_T7-1_short-i701_orig, T7-nXTv2_i5-1, 5X tn5059, NTC
KAPA SYBR FAST qPCR mix until saturation, X35 cycles

25 uL kapa sybr fast
4  uL scT7_S5XX index primer, 2 uL F, (i5XX_T7-1_long) USED XXX
4  uL nXTv2_i7XX index primer, 2 uL R, (i7XX_long or i7XX_orig)
5  uL N-H2O
12 uL DNA template (use half RT reaction)
_____________
50 uL

KAPA SYBR cycles:
72C 3m, 95C 30s, (95C for 10s, 59C for 30s, 72C for 1 min) X15, 72C for 3 min, 4C forever

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


19. Pool all samples run on 6% PAGE gel, Qubit. Gel Size selection

  • gel size select from 220-1000 bp, follow gel size selection protocol
  • do not need to include controls.


Results[edit]

  • PCR curves

File:2015-09-29 tm change, and kapa sybr fast.bmp


  • TBE
  • worked better, probably because of kapa sybr fast. though band is still there at 250
  • smears also do not look as clean as 9/24/15 samples cleaned after tagmentation with DNA clean and concentrator

File:ZhangLab 2 2015-09-29 17hr 02min-labeled.jpg