RNA Quality Control

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Revision as of 12:39, 9 May 2007

Quality control of RNA

RNA Quality control This protocol will assist you in performing RNA quality control for a variet of purposes; Microarray, real-time and Northern analysis.

Checking RNA/cRNA samples on a nanodrop Spec

• Check concentration, A260/A280, A260/A230 on Nanodrop Spectrophotometer.
• Maintain the A260/A280 ratio close to 2.0 for pure RNA (ratios between 1.9 and 2.1 are acceptable).
• For Affymetrix labeling reactiosns; concentrations of cRNA are generally around 1000-1500ng/µl for a 40µl IVT reaction using 20µl of cDNA template.

Checking RNA/cRNA samples on an agilent bioanalyzer

Agilent BioAnalyzer Gel electrophoresis of the RNA is done to estimate the quality of the RNA. The bioanalyzer software produces a RIN (RNA integrity number) this gives a measure of sample quality that is not subjective. Howver it needs to be used with some caution and is not as useful as it sounds.

RNA Image galleries

The following are examples of typical Human RNA examined on an Agilent 2100 BioAnalyser. RNA electropherograms have different profiles depending on species, tissue and starting material quality.

Human RNA good quality	Human RNA slightly degraded.jpg Human RNA slightly degraded	Human RNA very degraded.jpg Human RNA very degraded	Human RNA brain.jpg Human RNA brain
Human RNA muscle.jpg Human RNA muscle	Human RNA blood.jpg Human RNA blood	Drosphila RNA good quality.jpg Drosphila RNA good quality	Arabidopsis RNA good quality
Arabidopsis RNA slightly degraded.jpg Arabidopsis RNA slightly degraded	Arabidopsis single cell aRNA	Barley RNA good quality	Wheat RNA good quality
Explanation of electropherograms.

cRNA Image galleries

The following are examples of typical cRNA products examined on an Agilent 2100 BioAnalyser. cRNA electropherograms have different profiles depending on species and starting material quality.

Affymetrix One cycle Human cRNA good quality	Affymetrix Two cycle Human cRNA good quality	Affymetrix one cycle Arabidopsis cRNA good quality	Affymetrix one cycle Arabidopsis single cell aRNA cRNA
Affymetrix one cycle Barley cRNA good quality	Affymetrix one cycle Wheat cRNA good quality	Affymetrix one cycle Wheat cRNA poor quality	Affymetrix Two cycle Human cRNA 100ng starting.jpg Affymetrix Two cycle Human cRNA 100ng starting
Affymetrix Two cycle Human cRNA 10ng starting.jpg Affymetrix Two cycle Human cRNA 10ng starting	Affymetrix Two cycle Human cRNA 5ng starting.jpg Affymetrix Two cycle Human cRNA 5ng starting	Affymetrix Two cycle Human cRNA 1ng starting.jpg Affymetrix Two cycle Human cRNA 1ng starting	Explanation of electropherograms.

Checking RNA/cRNA Samples on a denaturing formaldehyde gel

I still need to add a formaldhyde gel protocol, anyone else got one?

Contact

• mail to jamesdothadfieldatcancerdotorgdotuk
• This page was created by James Hadfield on 12 October 2006. I hope you found it useful.