Blue:RNA-Seq Experiments:09102013: Difference between revisions
Jump to navigation
Jump to search
>B1lake |
>B1lake |
||
Line 14: | Line 14: | ||
| align="center" style="background:#f0f0f0;"|'''Library Conc''' | | align="center" style="background:#f0f0f0;"|'''Library Conc''' | ||
|- | |- | ||
| BL_ERCC_N2id1_||ERCC||1ng - Fragmented||[http://genome-tech.ucsd.edu/LabNotes/index.php/Blue:RNAseq_Primer_List#totoRNA_5.27_primer_sequence TSO.r04]||[http://genome-tech.ucsd.edu/LabNotes/index.php/Blue:RNAseq_Primer_List#totoRNA_3.27_primer_sequence T20V.id1]||[http://genome-tech.ucsd.edu/LabNotes/index.php/Blue:RNAseq_Primer_List#totoRNA_3.27_primer_sequence N2.id1]||totoRNAseq|| | | BL_ERCC_N2id1_||ERCC||1ng - Fragmented||[http://genome-tech.ucsd.edu/LabNotes/index.php/Blue:RNAseq_Primer_List#totoRNA_5.27_primer_sequence TSO.r04]||[http://genome-tech.ucsd.edu/LabNotes/index.php/Blue:RNAseq_Primer_List#totoRNA_3.27_primer_sequence T20V.id1]||[http://genome-tech.ucsd.edu/LabNotes/index.php/Blue:RNAseq_Primer_List#totoRNA_3.27_primer_sequence N2.id1]||totoRNAseq||QC qPCR Analysis|| | ||
|- | |- | ||
| BL_ERCC_N2id2_||ERCC||1ng - Unfragmented||TSO.R04||T20V.id2||N2.id2|||||| | | BL_ERCC_N2id2_||ERCC||1ng - Unfragmented||TSO.R04||T20V.id2||N2.id2|||||| |
Revision as of 22:14, 9 September 2013
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_ERCC_N2id1_ | ERCC | 1ng - Fragmented | TSO.r04 | T20V.id1 | N2.id1 | totoRNAseq | QC qPCR Analysis | |
BL_ERCC_N2id2_ | ERCC | 1ng - Unfragmented | TSO.R04 | T20V.id2 | N2.id2 | |||
BL_ERCC_N2id3_ | ERCC | 1ng - Fragmented | TSO.R05 | T20V.id3 | N2.id3 | |||
BL_ERCC_N2id4_ | ERCC | 1ng - Unfragmented | TSO.R05 | T20V.id4 | N2.id4 | |||
BL_ERCC_N2id5_ | ERCC | 1ng - Fragmented | Smarter TSO | T20V.id5 | N2.id5 | |||
BL_ERCC_N2id6_ | ERCC | 1ng - Unfragmented | Smarter TSO | T20V.id6 | N2.id6 | |||
BL_ERCC_N2id7_ | ERCC | 1ng - Fragmented | TSO.R04 | Supp.T20.id7 | N2.id7 | |||
BL_ERCC_N2id8_ | ERCC | 1ng - Unfragmented | TSO.R04 | Supp.T20.id8 | N2.id8 |
Plate Layout: Samples and Indexes
' | 1 | 2 | 3 |
A | NC(1) | UHRR(9) | Nc(17) |
B | Sc(2) | Sc(10) | Sc(18) |
C | Sc(3) | Sc(11) | Sc(19) |
D | Sc(4) | Sc(12) | Sc(20) |
E | Sc(5) | Sc(13) | Sc(21) |
F | Sc(6) | Sc(14) | Sc(22) |
G | Sc(7) | Sc(15) | Sc(23) |
H | Sc(8) | Sc(16) | 10cells(24) |
Note: SC=Single cell; UHRR=Universal Human Reference RNA
Cells Sorted 08302013
Purpose
- Repeat Single cell RNAseIII/TSO totoRNAseq protocol last used on 08202013
- Generate totoRNAseq libraries for single human NSCs
Library Preparation (totoRNAseq):
- Cell Sort
Volume RNA 250pg or Single Cells - 1x Lysis Buffer 0.4ul Total 0.4ul
Note: add in UHRR control at this point
- RNA FRAGMENTATION
Volume RNA 0.4ul 10x RNaseIII Buffer 0.2ul 0.1uM T20V.id 0.1ul dH20 0.55ul Total 1.25ul
- Incubate @ 72C 3 min
- Incubate @ 37C 1min
- Incubate @ 4C 10min
- RNA FRAGMENTATION
Volume RNA 1.25ul RNase III 0.08ul dH20 0.67ul Total 2ul
- Incubate @ 37C 10 min
- Add 1.1ul dH2O
- Incubate @ 65C 10 min
- 3' Tailing
Volume PNK_fRNA 3.1ul 5x RT Buffer 0.5ul 1mM ATP 0.25ul 0.5U/ul PAP (1:10d in H2O) 0.25ul
- Incubate @ 37C 5 min
- Transfer to Ice
- Reverse Transcription
Volume PAP RNA 4.1ul 10mM dNTP Mix 1ul 0.1uM T20V.ID 0.9ul
- Incubate @ 65C 3 min
- Transfer to Ice
Volume 5xRT Buffer 1.5ul 100mM DTT 0.17ul Betaine (5M) 2ul RNase Inhibitor (40U/ul) 0.1ul Smarter MMLV (200U/ul) 0.23ul Total 10ul
- Incubate @ 42C 30 min
- Beads Purification
- Add 15ul beads per well
- Allow to bind 15 min
- Combine all odd or even column wells
- Remove supernatant and wash 2x with 1ml 80% EtOH
- Air Dry 10min or until cracking first occurs
- Resuspend beads in 20ul dH2O, incubate 2min, transfer to new tube
- Vacuspin room temperature for 10+min to bring volume to 6ul (TSO)
TSO
- TSO (x2)
Volume Purified cDNA 3ul 5x RT buffer [MMLV] 2ul 10mM dNTP mix 1ul 100mM DTT 0.25ul 10uM TSO.r04 1ul Betaine (5M) 2ul RNase Inhibitor 0.25ul Smarter MMLV 0.5ul Total 10ul
- Incubate @42C 10min
- Incubate @70C 10min
- USER
- Add 1ul and incubate at 37C for 30 min
- PCR (PhusionHF)
Volume TSO Reaction 11ul 2x Buffer 25ul 10uM PB_PCR_F 1ul 10uM PCR_N2_idX 1ul H2O 12ul Total 50ul
98C 30 sec 98C 15s -> 58C 20s -> 72C 30s 6x 98C 10s -> 72C 20s 15x 72C, 5min
- Ampure Beads Purify (0.8x)
- Resuspend in 50ul
- Ampure Beads Purify (0.8x)
- Resuspend in 10ul
Results of Amplification
- Ran 1ul on gel:
Final Library Preparation
- Re-Amplified 1ul using Sybr-Green and ILMN_PCR_F/R
Volume Library 1ul 2xSybr Buffer 25ul 10uM ILMN_PCR_F 1ul 10uM ILMN_PCR_R 1ul dH2O 22ul Total 50ul
- 95C 30sec
- 95C 10s -> 60C 20s -> 72C 30s => 5X
- 72C, 5min
- Ampure Beads purified (0.8x)
- Resuspended in 10ul and ran 1 ul on gel: