Arichard:Notebook/2013/June: Difference between revisions

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* Both samples had 1 ul of 1:500 dilution of 100 mM dUTP during final PCR (107 ul total volume).
* Both samples had 1 ul of 1:500 dilution of 100 mM dUTP during final PCR (107 ul total volume).


====Quartz-Seq Protocol for 500 pg Agilent UHRR====
====Quartz-Seq Protocol for 500 pg Agilent UHRR, 2 samples====
 
* Work in the PCR hood
* Keep enzyme stocks in cold box
* Mix reactions on cold rack
* Use UV treated Ambion RNase/DNase free water
* Use UV treated 0.5 and 1.5 ml Eppendorf Lo-Bind tubes
* Use UV treated 0.2 ml Axygen Cat# 22-154LR low retention tubes


* UHRR/ERCC mix:
* UHRR/ERCC mix:
Line 65: Line 72:
# Hold @ 4 degC
# Hold @ 4 degC


* RT rxn (mix on cold rack):
* RT rxn:
** 12 ul RT annealing rxn
** 12 ul RT annealing rxn
** 8 ul RT rxn mix
** 8 ul RT rxn mix
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# 10 min @ 70 degC
# 10 min @ 70 degC
# Hold at 4 degC
# Hold at 4 degC
# Prepare Exo I mix
* Exo I mix:
** 2 ul 10X Titanium Taq buffer
** 1 ul 10X Exo III buffer
** 1 ul 0.1 M DTT
** 3 ul Exo I
** 23 ul H2O
* Total = 30 ul
* RT primer removal:
** 20 ul RT rxn
** 36 ul Ampure RNAClean XP
* Total = 56 ul
# 10 min @ RT
# 5 min on magnet
# Wash 2x with 1 min with 50 ul 80% EtOH
# Dry 3 min
# Add 6 ul Exo I mix
# 1 min @ RT
# 5 min on magnet
# Transfer to new tube
# 30 min @ 37 degC
# 20 min @ 80 degC
# Hold @ 4 degC
WIP
* PolyA mix:
** 1 ul 10X Titanium Taq buffer
* Total = 10 ul


WIP




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[[File: 2013_06_26 quartz seq 500 pg uhrr.jpd|400px]]
[[File: 2013_06_26 quartz seq 500 pg uhrr.jpd|400px]]


==June 27, 2013===
===June 27, 2013===

Revision as of 22:22, 27 June 2013

June 2013

June 2, 2013

File:2013 06 02 hela5before.tif Cell 5, HeLa, before expelling onto glass top tube cap

File:2013 06 02 hela5after.tif Cell 5, HeLa, after expelling. The cell here is in the lower left of center. The other two objects are appear small, irregular, and shriveled as the focal plane is moved through them. This is difficult to convey in a single image.

File:2013 06 02 hela6before.tif Cell 6, HeLa, before expelling

File:2013 06 02 hela6after.tif Cell 6, HeLa, after expelling. There legitimately appears to multiple cells in this droplet.

  • These samples were diluted to ~10,000 cells/ml --> 10 cells/ul. More dilution might help avoid picking multiple cells, but other technical challenges remain.
  • After depositing the cell on the glass top tube cap, there is only ~10 seconds before the droplet dries (~100 nl maximum volume by my estimate, although variance is large.) This is hardly enough time to image the cell.
  • The CEL-Seq paper refers to "pipetting off excess liquid." I haven't tried this yet. I could deposit the cell in a larger volume, and then adjust the volume down. This issue here would be finding the cell in that larger volume (if I fail to see it shoot out of the pipette.) Also, the omnipresent dust particle and cell debris make imaging the cells very hard in BF.
  • I should probably wash the cells after thawing.

June 5, 2013

June 5, 2013 progress report

June 25, 2013

  • Implemented Quartz seq, Samples A1 and A2.
    • Sample A1: 500 pg UHRR, CEL-Seq equivalent ERCC, Quartz purified RNA protocol. Used 2x Terra Direct PCR Mix.
    • Sample A2: Same, except I used 2x KAPA HiFi Uracil+.
  • Both samples had 1 ul of 1:500 dilution of 100 mM dUTP during final PCR (107 ul total volume).

Quartz-Seq Protocol for 500 pg Agilent UHRR, 2 samples

  • Work in the PCR hood
  • Keep enzyme stocks in cold box
  • Mix reactions on cold rack
  • Use UV treated Ambion RNase/DNase free water
  • Use UV treated 0.5 and 1.5 ml Eppendorf Lo-Bind tubes
  • Use UV treated 0.2 ml Axygen Cat# 22-154LR low retention tubes
  • UHRR/ERCC mix:
    • 2.5 ul 500 pg/ul UHRR
    • 2.5 ul 1:1e4 ERCC
    • 14 ul H2O
  • Total = 19 ul
  • RT annealing mix:
    • 3 ul 10X Titanium Taq buffer
    • 3 ul 1 mM dNTPs
    • 3 ul 0.833 uM RT primer
    • 2 ul RNasin Plus
    • 19 ul UHRR/ERCC mix
  • Total = 30 ul
  • RT rxn mix:
    • 2 ul 10X Titanium Taq buffer
    • 13 ul H2O
    • 2.5 ul 0.1 M DTT
    • 2.5 ul SuperScript III
  • Total = 20 ul
  • RT annealing rxn:
    • 12 ul RT priming buffer (Quartz seq adds this to beads, but we are using purified reference RNA in the priming buffer)
  • Total = 12 ul
  1. 1 min @ RT
  2. 90 sec @ 70 degC
  3. 15 sec @ 35 degC
  4. Hold @ 4 degC
  • RT rxn:
    • 12 ul RT annealing rxn
    • 8 ul RT rxn mix
  • Total = 20 ul
  1. 5 min @ 35 degC
  2. 20 min @ 45 degC
  3. 10 min @ 70 degC
  4. Hold at 4 degC
  5. Prepare Exo I mix
  • Exo I mix:
    • 2 ul 10X Titanium Taq buffer
    • 1 ul 10X Exo III buffer
    • 1 ul 0.1 M DTT
    • 3 ul Exo I
    • 23 ul H2O
  • Total = 30 ul
  • RT primer removal:
    • 20 ul RT rxn
    • 36 ul Ampure RNAClean XP
  • Total = 56 ul
  1. 10 min @ RT
  2. 5 min on magnet
  3. Wash 2x with 1 min with 50 ul 80% EtOH
  4. Dry 3 min
  5. Add 6 ul Exo I mix
  6. 1 min @ RT
  7. 5 min on magnet
  8. Transfer to new tube
  9. 30 min @ 37 degC
  10. 20 min @ 80 degC
  11. Hold @ 4 degC

WIP

  • PolyA mix:
    • 1 ul 10X Titanium Taq buffer
  • Total = 10 ul

WIP


June 26, 2013

  • Library prep for Quartz-seq samples A1 and A2:
    • Adapter ligation using KAPA Rapid Ligation, USER, and PCR with KAPA SYBR Fast (See Jeff and Noi's protocols [need link]).

File:2013 06 26 quartz seq 500 pg uhrr.jpd

June 27, 2013