Arichard:Protocols/CEL Seq: Difference between revisions
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## Add 1 ul 100 ng/ul RNA to 9 ul H2O --> 10 ul 10 ng/ul RNA. | ## Add 1 ul 100 ng/ul RNA to 9 ul H2O --> 10 ul 10 ng/ul RNA. | ||
## Add 2 ul 10 ng/ul RNA to 8 ul of H2O --> 10 ul 2 ng/ul RNA. | ## Add 2 ul 10 ng/ul RNA to 8 ul of H2O --> 10 ul 2 ng/ul RNA. | ||
# Dilute ERCC RNA Spike-in Control to 1:10,000, on ice: | |||
## Add 1 ul of undiluted ERCC to 9 ul H2O --> 10 ul 1:10 ERCC. | |||
## Add 1 ul of 1:10 ERCC to 9 ul H2O --> 10 ul 1:100 ERCC. | |||
## Add 1 ul of 1:100 ERCC to 9 ul H2O --> 10 ul 1:1000 ERCC. | |||
## Add 1 ul of 1:1000 ERCC to 9 ul H2O --> 10 ul 1:10000 ERCC. | |||
# Add 5 ul 2 ng/ul RNA to 2 ul 1:10000 ERCC --> 7 ul 1.42 ng/ul RNA 1:35000 ERCC. | |||
## Add 0.7 ul of this to 0.5 ul 32 pmol/ul primer for 1 ng total RNA samples. | |||
## Need total of 2 x 0.7 ul + 2 ul for dilution to 142 pg/ul RNA 1:350000 ERCC = 3.4 ul. | |||
# Add 2 ul 1.42 ng/ul RNA 1:35000 ERCC to 18 ul H2O --> 20 ul 142 pg/ul RNA 1:350000 ERCC. | |||
## Add 0.7 ul of this to 0.5 ul 3.2 pmol/ul primer for 100 pg total RNA samples. | |||
## Need 14 x 0.7 ul + 1 ul for dilution to 14.2 pg/ul RNA 1:3500000 ERCC = 10.8 ul. | |||
# Add 1 ul 142 pg/ul RNA 1:350000 ERCC to 9 ul H2O --> 10 ul 14.2 pg/ul RNA 1:3500000 ERCC. | |||
## Add 0.7 ul of this to 0.5 ul 0.32 pmol/ul primer for 10 pg samples. | |||
## Need 12 x 0.7 ul = 8.4 ul. |
Revision as of 00:52, 8 February 2013
CEL-Seq protocol validation
- Protocol modified to use common sequence primer with Illumina 5' Adapter and T7 promoter (CS-5primeAD-T7).
- 100 ng/ul total RNA will be used as input (from Rui).
- I will work with 16 tubes at a time.
- For one set of 16 tubes, I want 2 x 1 ng rxns (+ control), 12 x 100 pg rxns (experimental), and 2 x no RNA (no template controls, NTC).
- For the second set of 16, I want 2 x 100 pg rxns (+ control), 12 x 10 pg rxns (experimental, approx. single cell amount), and 2 x no RNA (NTCs).
- Keep all RNA on ice at all times.
- Work in the hood. EtOH, RNase away, and UV treat all surfaces and tools. UV treat water for dilutions.
- Use low-bind tubes.
Prep
- Sample layout is as follows:
Sample # | RNA input | Sample # | RNA input | Sample # | RNA input | Sample # | RNA input |
1 | 1 ng | 9 | 100 pg | 17 | 100 pg | 25 | 10 pg |
2 | 1 ng | 10 | 100 pg | 18 | 100 pg | 26 | 10 pg |
3 | 100 pg | 11 | 100 pg | 19 | 10 pg | 27 | 10 pg |
4 | 100 pg | 12 | 100 pg | 20 | 10 pg | 28 | 10 pg |
5 | 100 pg | 13 | 100 pg | 21 | 10 pg | 29 | 10 pg |
6 | 100 pg | 14 | 100 pg | 22 | 10 pg | 30 | 10 pg |
7 | 100 pg | 15 | NTC | 23 | 10 pg | 31 | NTC |
8 | 100 pg | 16 | NTC | 24 | 10 pg | 32 | NTC |
- Barcoded RT primers are in 48 wells of a 92 well plate at 200 uM each, in the following layout:
Barcode number | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
A | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
B | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 |
C | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 |
D | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 |
E | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty |
F | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty |
G | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty |
H | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty | Empty |
- Serial dilutions will be necessary to dilute the RT primers to the correct concentration.
Dilute RT primers to appropriate concentrations
- Dilute primers to 32 pmol/ul, 3.2 pmol/ul, and 0.32 pmol/ul, depending on input (Note that each primer must be diluted separately for each sample):
- Add 16 ul of 100 pmol/ul primer to 84 ul H2O --> 100 ul 32 pmol/ul primer. Use 0.5 ul of this per 1 ng total RNA.
- Add 10 ul of 32 pmol/ul primer to 90 ul H2O --> 100 ul 3.2 pmol/ul primer. Use 0.5 ul of this per 100 pg total RNA.
- Add 10 ul of 3.2 pmol/ul primer to 90 ul H2O --> 100 ul 0.32 pmol/ul primer. Use 0.5 ul of this per 10 pg total RNA.
- Dilute total RNA to 2 ng/ul, on ice:
- Add 1 ul 100 ng/ul RNA to 9 ul H2O --> 10 ul 10 ng/ul RNA.
- Add 2 ul 10 ng/ul RNA to 8 ul of H2O --> 10 ul 2 ng/ul RNA.
- Dilute ERCC RNA Spike-in Control to 1:10,000, on ice:
- Add 1 ul of undiluted ERCC to 9 ul H2O --> 10 ul 1:10 ERCC.
- Add 1 ul of 1:10 ERCC to 9 ul H2O --> 10 ul 1:100 ERCC.
- Add 1 ul of 1:100 ERCC to 9 ul H2O --> 10 ul 1:1000 ERCC.
- Add 1 ul of 1:1000 ERCC to 9 ul H2O --> 10 ul 1:10000 ERCC.
- Add 5 ul 2 ng/ul RNA to 2 ul 1:10000 ERCC --> 7 ul 1.42 ng/ul RNA 1:35000 ERCC.
- Add 0.7 ul of this to 0.5 ul 32 pmol/ul primer for 1 ng total RNA samples.
- Need total of 2 x 0.7 ul + 2 ul for dilution to 142 pg/ul RNA 1:350000 ERCC = 3.4 ul.
- Add 2 ul 1.42 ng/ul RNA 1:35000 ERCC to 18 ul H2O --> 20 ul 142 pg/ul RNA 1:350000 ERCC.
- Add 0.7 ul of this to 0.5 ul 3.2 pmol/ul primer for 100 pg total RNA samples.
- Need 14 x 0.7 ul + 1 ul for dilution to 14.2 pg/ul RNA 1:3500000 ERCC = 10.8 ul.
- Add 1 ul 142 pg/ul RNA 1:350000 ERCC to 9 ul H2O --> 10 ul 14.2 pg/ul RNA 1:3500000 ERCC.
- Add 0.7 ul of this to 0.5 ul 0.32 pmol/ul primer for 10 pg samples.
- Need 12 x 0.7 ul = 8.4 ul.