Blue:RNA-Seq Experiments:11122013

From ZhangLabWiki
Revision as of 22:10, 12 November 2013 by >B1lake (→‎Purpose)
Jump to navigation Jump to search

RNA-Seq Library Information

Library ID Samples Input RNA TSO Primer Bar Code Primers Bar Code Primer 2 Type of Seq Reads Library Conc
BL_ UHRR/ERCC 10ng - RNase3 (5mM MnCl2)/PAP (2.5mM MnCl2) 10min ATP TSO.r06 T20VN_PE_R N2.id81 totoRNAseq
BL_ UHRR/ERCC 10ng - RNase3 (5mM MnCl2)/PAP (2.5mM MnCl2) 10min ATP/dATP TSO.r06 T20VN_PE_R N2.id82 totoRNAseq
BL_ UHRR/ERCC 10ng - RNase3 (5mM MnCl2)/PAP (2.5mM MnCl2) 30min ATP/dATP TSO.r06 T20VN_PE_R N2.id83 totoRNAseq
BL_ UHRR/ERCC 10ng - RNase3 (10mM MnCl2)/PAP (5mM MnCl2) 10min ATP TSO.r06 T20VN_PE_R N2.id84 totoRNAseq
BL_ UHRR/ERCC 10ng - RNase3 (10mM MnCl2)/PAP (5mM MnCl2) 10min ATP/dATP TSO.r06 T20VN_PE_R N2.id85 totoRNAseq
BL_ UHRR/ERCC 10ng - RNase3 (10mM MnCl2)/PAP (5mM MnCl2) 30min ATP/dATP TSO.r06 T20VN_PE_R N2.id86 totoRNAseq
BL_ UHRR/ERCC 10ng - RNase3 (20mM MnCl2)/PAP (10mM MnCl2) 10min ATP TSO.r06 T20VN_PE_R N2.id87 totoRNAseq
BL_ UHRR/ERCC 10ng - RNase3 (20mM MnCl2)/PAP (10mM MnCl2) 10min ATP/dATP TSO.r06 T20VN_PE_R N2.id88 totoRNAseq
BL_ UHRR/ERCC 10ng - RNase3 (20mM MnCl2)/PAP (10mM MnCl2) 30min ATP/dATP TSO.r06 T20VN_PE_R N2.id89 totoRNAseq

Purpose

  • Full totoRNAseq protocol on samples prepared similarly to 11-06-2013
  • Determine optimal PAP conditions for library production
  • Use T20VN to limit the primer annealing to the ends flanking RNA fragments rather than randomly along extensive poly(A) tails

RNAseIII-Fragmented Library Preparation

RNA
Volume
UHRR 20ng/ul 0.5ul
ERCC 1:10E3 0.2ul
1uM T20VN 0.1ul
dH2O 0.2ul
Total 1ul


Incubate @ 72C 3 min
Incubate @ 37C 1 min


Volume
5x Ambion PAP buffer 0.08ul
MnCl2 0.4ul
RNase III 0.1ul
dH20 0.42ul
Total 2ul


Incubate @ 37C 5 min


3' Tailing
Volume
fRNA 2ul
5x Ambion PAP Buffer 0.72ul
1mM ATP (or mix) 0.25ul
2U/ul PAP 0.2ul
40U/ul Rnase Inhibitor 0.2ul
dH2O 0.63ul
Total 4ul


Incubate @ 37C 10 min - 30 min
Add 0.5ul of 2uM T20VN


Reverse Transcription
Volume
PAP RNA 4.5ul
5xRT Buffer 2ul
10mM dNTP Mix 1ul
100mM DTT 0.25ul
Betaine (5M) 2ul
Smarter MMLV (200U/ul) 0.25ul
Total 10ul


Incubate @ 42C 30 min


Beads Purification
  1. Add 15ul beads per well
  2. Allow to bind 15 min
  3. Remove supernatant and wash 2x with 1ml 80% EtOH
  4. Air Dry 10min or until cracking first occurs
  5. Resuspend beads in 3ul dH2O, incubate 2min, transfer to new tube


TSO
Volume
Purified cDNA 3ul
5x RT buffer [MMLV] 2ul
10mM dNTP mix 1ul
100mM DTT 0.25ul
10uM TSO 1ul
Betaine (5M) 2ul
RNase Inhibitor 0.25ul
Smarter MMLV 0.5ul
Total 10ul


Incubate @42C 10min
Incubate @70C 10min


PCR (PhusionHF)
Volume
TSO Reaction 10ul
2x Buffer 25ul
10uM P1-STRT 1ul
10uM PCR_R_N2_id 1ul
H2O 13ul
Total 50ul


98C 30 sec
98C 15s -> 58C 20s -> 72C 30s 6x
98C 10s -> 72C 20s 8x
72C, 5min

Results of Amplification

  • Run 5ul on gel:


Final Library Preparation

  • Beads purified twice at (0.8x), re-suspend in 10ul