Technique / Molecular Biology / RNA transcriptional and post-transcriptional regulation
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DNase I hypersensitivity assay (1)
Northern blot hybridization (3)
Nuclear run-on assay (1)
Primer extension (6)
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RNA methods from scienceboard.net
new
protocol
Protocol from Scientific Advisory Board (scienceboard.net).
content
10/17/2003 RNA from tissues.
10/17/2003 Total cellular RNA
10/17/2003 EXTRACTION AND PURIFICATION OF TOTAL RNA USING TRIzol
10/19/2003 Native Gel Electrophoresis of R ...
mRNA purification protocol
new
protocol
mRNA purification protocol from Breeden's lab. The mRNA purification steps include preparing oligo-dT cellulose column, total RNA elution and washing in the oligo-dT cellulose column, precipitation and recovering of mRNA. Buffer recipes for mRNA purification a ...
Differential display of mRNA analysis (Breeden's lab)
protocol
Differential display of mRNA analysis (Breeden's lab).
Protocol link ...
Methods to Remove DNA Contamination from RNA Samples
new
protocol
An ambion tech notes on how to remove DNA contamination from RNA preparations.
Genomic DNA false positive signals are easily identified by performing a "no-RT" control during RT-PCR. We can therefore assess the effectiveness of DNA removal methods by agaros ...
In Vitro Transcription Reverse Transcription
new
protocol
PDF prootcol by Paul Kroeger from Marimoto lab at Northwestern University. ...
Nonsense-mediated mRNA decay (NMD)
new recommended
review
Nonsense-mediated mRNA decay (NMD) is a mRNA degradation mechanism that eliminates mRNA containing premature translation-termination codons (PTC) usually at 55bp upstream of the exon junction complex (EJC). The NMD process is tightly coupled with translation a ...
Ten Ways to Improve Your RNA Isolation
review
A tech notes from Ambion. It gives suggestions on following ten aspects:
1. Use proper cell or tissue storage conditions.
2. Thoroughly homogenize samples.
3. Pretreat homogenate before RNA isolation.
4.Choose the best RNA isolation method.
5. DNase tr ...
List of human house keeping gene
new
review
In this short review authors summarized use of human house keeping gene in gene expression study.
Human housekeeping genes are compact.
Eisenberg E, Levanon EY
Trends Genet. 2003 Jul ; 19(7): 362-5
This web page lists all popular house keeping genes b ...
TechNote on Working with RNA
new
review
A technique bulletin describing the general guidance on working with RNA (Ambion Inc.).
- Living with RNase.
- RNA storage.
- RNA precipitate
- RNA radioactivity incorporation and yield. ...
Plasmid DNA extraction from e.coli for digestion mapping clony screening
new
review
Plasmid DNA extraction from e.coli for digestion mapping clony screening:
This protocol utilize the Qiagen buffer P1, P2 and P3 from Qiagen
plasmid purification kit. RNase must be added before use. It is cost
efficient since it doesn't use expensive plasm ...
Redissolving RNA Pellet
troubleshooting
I am working with total RNA from Chondrocyte cells. I am isolating the
RNA using TRizol Reagent and I am having a problem with the last step of
redissolving the RNA pellet. These cells have been put in 1.2% alginate
and cultured for 5 days and then ex ...
mRNA isolation kits
troubleshooting
I want to isolate mRNA from human B-Lymphocyte cell lines. Could somebody
suggest some mRNA isolation kits which has given good yields. I will be
using the mRNA for RT-PCR. ... ...
...
DNA contamination in RNA sample
troubleshooting
I'm trying to look for a efficient method to remove the DNA contamination in my total RNA samples. I'm working with a Gram-positive bacteria E. hirae and I'm trying to use the RNA for quantitative RT-PCR.
I've used both the Gaunidium thiocyanate method an ...
how to make nuclease free water ?
troubleshooting
could anybody provide me with a short protocol on how to prepare nuclease
free water? I need it for PCR, RT-PCR and RNA extraction from plant tissues.
We have a milli-Q system and I don't want to use DEPC. ... ...
...
total RNA measurement
troubleshooting
what would be a best choice of RNA standard (origin, size, etc., maybe
even catalog #?) when comparing total RNA content in different species
(both pro- and eucaryotes). ... ...
...
RNA extraction
troubleshooting
I have isolated total RNA from non adherent cells with the TRIZOL reagent.
At the end of the procedure, I solubilized the pellet with DEPC-treated
water. After this, I measured OD 260 and 280 and calculated the ratio
260/280. This ratio should be 1.6 ...
Small scale TRIZOL extraction
troubleshooting
I'd very much appreciate if somebody lets me know a recommended volume of
TRIZOL for small size samples (10-20ul).
Click here for replies to this question ...
General reverse transcription troubleshooting guide
new
troubleshooting
Low cDNA yield:
1. Check reverse transcription temperature. Different reverse transcriptase may require different reaction temperature, ranging from 37c to 65c.
2. RNA template is degraded or concentration is wrong. Use RNase inhibitor in the reac ...
RNA analysis tools and programs
new
software
This is a collection of RNA analysis tools from Pasteur Institute BioWeb.
MFOLD: prediction of RNA Secondary Structure by Energy Minimization (Zuker) (advanced form)
Vienna RNA package (documentation)
RNAfold: calculate secondary structures of RNAs (adv ...
Antisense technonology animation
media
Flash antisense technonology animation.(University of Nebraska - Lincoln) ...
()
RNA can be purified in either total RNA or poly(A)-selected RNA (mRNA) form. mRNA comprises less than 5% of cellular total RNA. Generally speaking, for most RNA related applications, total RNA is sufficient for most requirements. Two specific applications, cDNA library construction and cDNA labeling for microarray require isolation of mRNA. Around 30ug of mRNA equels 1mg of total RNA.
Northern blot hybridization is used for determination of mRNA molecular weight and relative abundance. It is commonly performed using total RNA. Dot hybridization can not determine the size of mRNA species but can assay the quatity of the RNA target. Ribonuclease protection assay is also used to assy the abundance of mRNA species. RT-PCR is the most sensitive method for quantitatively measureing of mRNA expression level.
Last update: 
01-Mar-2010 08:53 pm
Analysis of wide-domain transcriptional regulation in solid-state cultures of Aspergillus oryzae.
J Ind Microbiol Biotechnol. 2010 Feb 10; Authors: McKelvey SM, Murphy RA