AllPrep DNA/RNA Kits

For simultaneous purification of DNA and RNA from cells and tissues, including small samples, in spin-column and 96-well format

Features

  • High-quality DNA and RNA from the same sample
  • Maximal yields of DNA and RNA from precious samples
  • Rapid purification with short, streamlined protocol
  • Streamlined protocols for 96-well plates
  • Ready-to-use DNA and RNA for any downstream analysis
AllPrep DNA/RNA Micro Kit

Cat. No. / ID: 80284

For 50 micropreps: AllPrep DNA Spin Columns, RNeasy MinElute Spin Columns, Collection Tubes, Carrier RNA, RNase-Free Water and Buffers
Column typePlate type
Micro
Mini
96 well
The AllPrep DNA/RNA Kits is intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.

Product Details

AllPrep DNA/RNA Kits enable simultaneous purification of genomic DNA and total RNA from each cell or tissue sample. Since there is no need to divide each sample into two for separate purification procedures, maximum yields of DNA and RNA can be achieved. The purified DNA and RNA are eluted separately.

The AllPrep DNA/RNA Micro and Mini Kits can be automated on the QIAcube Connect. The AllPrep DNA/RNA 96 Kit is well suited for high-throughput purification of genomic DNA and total RNA from up to 96 samples.

Performance

Small samples of cultured cells and easy-to-lyse tissues can be processed with AllPrep DNA/RNA technology (see table “Optimal yields of DNA and RNA from tissues using the AllPrep DNA/RNA Micro Kit”). Genomic DNA is purified using the novel AllPrep DNA spin column, and total RNA is purified using an RNeasy MinElute spin column. Total RNA with Agilent RIN values of close to 10 is routinely obtained from cultured cells. Genomic DNA and total RNA show reliable quantification over a wide dynamic range (see figure " Wide dynamic range").

Optimal yields of DNA and RNA from tissues using the AllPrep DNA/RNA Micro Kit

Tissue (5 mg) DNA yield (µg)* RNA yield (µg)*
Heart 3.89 2.00
Brain 2.60 3.08
Kidney 11.33 12.70
Liver 32.40 16.02
Lung 9.65 24.63
Spleen 20.50 43.51
Thymus 34.90 56.89
Intestine 26.71 27.38

A simple workflow allows DNA and RNA extraction from one sample. The purified genomic DNA has an average length of 15–30 kb and performs well in multiplex PCR (see figure  "Multiplex PCR of 8 targets"). Total RNA is of high quality and has a RIN value of 10 indicating that the RNA is intact (see figure " Simultaneous purification of total RNA and genomic DNA" and figure " High-quality total RNA").

AllPrep DNA/RNA technology also enables efficient purification of high-quality DNA and RNA from different cell and tissue types in convenient 96-well format (see table “High-quality RNA from tissues purified using the AllPrep DNA/RNA 96 Kit” and figure " Reproducible purification of DNA and RNA in 96-well format").

High-quality RNA from tissues purified using the AllPrep DNA/RNA 96 Kit

Rat tissue RIN value*
Liver 9.4
Lung 9.5
Spleen 9.6
Thymus 10.0

There is no need for additional RNase or DNase digestion (see figure " RNA with no genomic DNA contamination") and the purified DNA is suitable for downstream applications (see figure " High-quality DNA for reliable multiplex PCR analysis").

See figures

Principle

AllPrep DNA/RNA Kits are designed to purify both genomic DNA and total RNA from the same cell or tissue sample. Since there is no need to divide the sample into two for separate purification procedures, maximum yields of DNA and RNA can be achieved. Efficient purification of high-quality DNA and RNA from different tissue types is achieved without the need for additional RNase or DNase digestion. The purified DNA and RNA are eluted separately and ready to use in any downstream application. Processing in 96-well format makes AllPrep DNA/RNA technology the ideal tool for sample preparation in genomics and systems biology.

Procedure

A simple spin-column workflow allows the purification of high-quality DNA and RNA from the same sample (see flowchart “ AllPrep DNA/RNA procedure”). Both cultured cells and easy-to-lyse tissues can be processed. Genomic DNA is purified using the novel AllPrep DNA spin column, and total RNA is purified using an RNeasy Mini or RNeasy MinElute spin column (AllPrep DNA/RNA Micro Kit).


When disrupting and homogenizing tissues in Buffer RLT Plus (supplied with the AllPrep DNA/RNA Micro Kit and Allprep DNA/RNA Mini Kit), excessive foaming may occur (please note this is not the case for the Allprep DNA/RNA 96 Kit since this product is supplied with Buffer RLT). This foaming is substantially reduced by adding Reagent DX (supplied separately) to Buffer RLT Plus at a final concentration of 0.5% (v/v) before starting disruption and homogenization. Reagent DX has been carefully tested with the kits, and has no effect on RNA purity or on downstream applications such as real-time RT-PCR. Buffer RLT Plus containing Reagent DX can be stored at room temperature (15–25ºC) for at least 9 months.

A supplementary protocol allows optional purification of protein. For experiments where DNA, RNA, and protein are regularly prepared from each sample, the AllPrep DNA/RNA/Protein Mini Kit can be used instead.

For high-throughput processing, the 96-well purification plates of the AllPrep DNA/RNA 96 Kit are for both DNA and RNA. The plates are rapidly and conveniently processed using either a centrifuge (Centrifuge 4-16 and Plate Rotor 2 x 96) or a combination of vacuum (QIAvac 96) and centrifuge. Both cultured cells and easy-to-lyse tissues can be processed.

AllPrep DNA/RNA Kits form part of QIAGEN's solution for preparing multiple analytes from the same sample. These include Allprotect Tissue Reagent, which stabilizes DNA, RNA, and protein in tissues, and RNAprotect Cell Reagent, which stabilizes DNA and RNA in cells. Both reagents deliver immediate stabilization at room temperature. For tissues, TissueRuptor and TissueLyser systems provide fast disruption at low- to high-throughputs.

See figures

Applications

The purified genomic DNA has an average length of 15–30 kb, depending on homogenization conditions, and is suited for any application, including next-generation sequencing, Southern-, dot-, and slot-blot analyses; and PCR and multiplex PCR.

The purified total RNA can be used in any application, such as RNA-seq RT-PCR and real-time RT-PCR; differential display; cDNA synthesis; northern-, dot-, and slot-blot analyses; and microarrays.

A supplementary protocol allows optional purification of protein. The purified protein is denatured and can be used in applications such as SDS-PAGE, western blotting, and 2D gel electrophoresis.

Comparison of AllPrep DNA/RNA Kits

Features AllPrep DNA/RNA Micro Kit AllPrep DNA/RNA Mini Kit AllPrep DNA/RNA 96 Kit
Applications PCR, RT-PCR, real-time PCR,
cDNA synthesis, microarray, blotting
PCR, real-time PCR, microarray,
blotting
PCR, real-time PCR, microarray,
blotting
Elution volume DNA: 30 µl; RNA: 10 µl 100 µl 50–100 µl
Format Spin column Spin column 96-well plate
Main sample type Cells, tissue Cells, tissue Cultured cells, easy-to-lyse tissue
Processing Manual (centrifugation) Manual (centrifugation) Manual (centrifugation and/or vacuum)
Purification of total RNA, miRNA,
poly A+ mRNA, DNA or protein
Genomic DNA and total RNA Genomic DNA and total RNA Total RNA, DNA, miRNA (optional)
Sample amount 5 x 105 cells or 5 mg tissue 1 x 107 cells or 30 mg tissue Up to 2 x 106 cells/up to 10 mg tissue
Technology Silica technology Silica technology Silica technology
Time per run or per prep 35 min 35 min 60 min
Yield Varies Varies Varies

Supporting data and figures

Resources

Kit Handbooks (3)
For simultaneous purification of genomic DNA and total RNA from the same small sample, including
  • animal and human cells (≤5 x 10^5)
  • animal and human tissues (≤5 mg)
  • microdissected cryosections
For simultaneous purification of genomic DNA and total RNA from animal and human cells and tissues in 96-well format
Brochures & Guides (1)

Publications

[The problem of tooth substitution].
Huber E;
Zahnarztl Mitt; 1975; 65 (1):1-2 1975 Jan 1 PMID:1096487
IgH gene rearrangements as plasma biomarkers in Non- Hodgkin's lymphoma patients.
He J; Wu J; Jiao Y; Wagner-Johnston N; Ambinder RF; Diaz LA Jr; Kinzler KW; Vogelstein B; Papadopoulos N;
Oncotarget; 2011; 2 (3):178-85 2011 Mar PMID:21399237
Application of microdroplet PCR for large-scale targeted bisulfite sequencing.
Komori HK; LaMere SA; Torkamani A; Hart GT; Kotsopoulos S; Warner J; Samuels ML; Olson J; Head SR; Ordoukhanian P; Lee PL; Link DR; Salomon DR;
Genome Res; 2011; 21 (10):1738-45 2011 Jul 14 PMID:21757609
Cell specific patterns of methylation in the human placenta.
Grigoriu A; Ferreira JC; Choufani S; Baczyk D; Kingdom J; Weksberg R;
Epigenetics; 2011; 6 (3):368-79 2011 Mar 1 PMID:21131778

FAQ

Can mitochondria separated with the Qproteome Mitochondria Isolation Kit be used for downstream DNA isolation?

Even though we have not tested this, we assume that both the QIAamp DNA Micro Kit and the AllPrep DNA/RNA Mini Kit will work to isolate DNA from mitochondria separated with the Qproteome Mitochondria Isolation Kit.

 

FAQ ID -1188
I received a kit containing the MinElute columns; however, they were left out for a while and not stored at 2–8°C upon receipt. Can I still use them?

The MinElute spin columns included in the following kits should be stored at 2–8°C upon arrival: AllPrep DNA/RNA Micro, EpiTect Fast DNA Bisulfite, EpiTect Fast FFPE Bisulfite, EpiTect Fast LyseAll Bisulfite, EpiTect Plus DNA Bisulfite, EpiTect Plus FFPE Bisulfite, EpiTect Plus LyseAll Bisulfite, exoRNeasy Serum/plasma Maxi, exoRNeasy Serum/Plasma Midi, GeneRead DNA FFPE, GeneRead rRNA Depletion, GeneRead Size Selection, MinElute Gel Extraction, MinElute PCR Purification, MinElute Reaction Cleanup, miRNeasy FFPE, miRNeasy Micro, miRNeasy Serum/Plasma, QIAamp DNA FFPE, QIAamp DNA Investigator, QIAamp DNA Micro, QIAamp MinElute Media, QIAamp MinElute Virus Spin, QIAamp MinElute Virus Vacuum, RNeasy FFPE, RNeasy Micro, RNeasy Plus Micro.

Short-term storage (up to 4 weeks) at room temperature (15–25°C) does not affect the performance. However, for optimal performance and quality, storage temperature should not exceed 25°C.

FAQ ID - 3560
How much sample can be used with the Allprep DNA/RNA 96 Kit?

Up to 1 x 10e6 cells or up to 5 mg tissue can be processed with the Allprep DNA/RNA 96 Kit when following the vacuum/spin protocol, or up to 2 x 10e6 cells or 10 mg tissue using the spin protocol.

 

FAQ ID -1997
What effect does homogenization have on DNA yield and integrity when using AllPrep DNA/RNA Kits?

Yield and integrity of genomic DNA depend on the disruption and homogenization method used with the Allprep DNA/RNA Kits.

Homogenization with the TissueRuptor (or other rotor–stator homogenizer, such as the Polytron) or the TissueLyser results in greater DNA fragmentation (depending on homogenization time and intensity). However, shorter DNA fragments are easier to elute, so DNA yields will be higher.

In contast, homogenization using the QIAshredder (or a syringe and needle) is more gentle, resulting in less DNA fragmentation. However, longer DNA fragments are more difficult to elute, so DNA yields may be lower.

 

FAQ ID -1751
Why does the Allprep DNA/RNA 96 Kit use Buffer RLT, whereas the AllPrep DNA/RNA Mini Kit uses Buffer RLT Plus?

The main difference between these buffers is that Buffer RLT Plus contains additional detergents. Buffer RLT Plus is optimized for efficient binding of DNA to the AllPrep DNA spin column. However, the AllPrep DNA 96 plate in the Allprep DNA/RNA 96 Kit behaves slightly different than the AllPrep DNA spin column in the AllPrep DNA/RNA Mini Kit, and achieves better specificity with Buffer RLT.

 

 

FAQ ID -1999
Which kit can be used for simultaneous purification of DNA and RNA from biopsies?

For easy-to-lyse tissues, AllPrep DNA/RNA Kits can be used. For biopsies of 5–30 mg, we recommend using the AllPrep DNA/RNA Mini Kit. For smaller biopsies, we recommend using the AllPrep DNA/RNA Micro Kit instead.

For examples of different cell lines and tissue types tested with these kits, and their average yields of DNA and RNA, please see Table 2 of the AllPrep DNA/RNA Micro and AllPrep DNA/RNA Mini Handbook.

 

 

FAQ ID -1089
Can acetone be used for precipitation of protein from Buffer RLT lysates generated with RNeasy Kits?

Yes, please follow the Supplementary Protocol Acetone precipitation of protein from Buffer RLT or Buffer RLT Plus lysates (RY22).

Important Note:

Do not use TCA to precipitate protein from Buffer RLT and Buffer RLT Plus lysates. These buffers contain guanidine thiocyanate, which can form highly reactive compounds when combined with acidic solutions.

 

For simultaneous purification of DNA, RNA, and protein from the same sample (either cultured cells or easy-to-lyse tissues), we recommend using the AllPrep DNA/RNA/Protein Mini Kit. This kit allows precipitation of protein from Buffer RLT lysates using a novel protein precipitation buffer, Buffer APP.

Please note that Buffer APP is not compatible with Buffer RLT Plus. Acetone should be used instead to precipitate protein from RLT Plus lysates.

 

FAQ ID -1164
How can foaming of Buffer RLT Plus lysates be avoided when using RNeasy Plus Micro and Mini Kits, or the Allprep DNA/RNA Mini Kit?

When using the RNeasy Plus Micro and RNeasy Plus Mini Kits, or the Allprep DNA/RNA Mini Kit, foaming of lysates can be substantially reduced by adding Reagent DX to Buffer RLT Plus at a final concentration of 0.5% (v/v) before starting sample lysis.

Reagent DX has been carefully tested with RNeasy Plus and Allprep Kits and has no effect on RNA purity or on downstream applications. Reagent DX can be purchased separately using catalog number 19088.

For more information on efficient sample disruption and homogenization for nucleic acid extractions, please see further product details and resources for the TissueRuptor, TissueLyser LT, and TissueLyser II.

FAQ ID -1734
Can the protocols for purification of small RNAs from cells in the appendices of the AllPrep DNA/RNA 96 Handbook also be used with tissue samples?

No. Tissue lysis generates more debris than cell lysis. This additional debris is not compatible with the special binding conditions for small RNAs using the Allprep DNA/RNA 96 Kit, and can lead to a reduction of up to 50% or more in RNA yield.

 

 

FAQ ID -2001
Will the "classic" RNeasy Mini Kit be discontinued after the launch of the Allprep DNA/RNA Mini Kit?

No, our standard RNeasy Mini Kit will not be discontinued. The Allprep DNA/RNA Mini Kit is an addition to our RNeasy product line.

 

 

FAQ ID -1054
What is Tissue-Tek O.C.T., and what is it used for?

Tissue-Tek O.C.T. is an embedding compound for cryosectioning, which is soluble in water. It mainly consists of glycols and synthetic resins. Tissue-Tek O.C.T. is used as matrix for cryosectioning of tissues. Using the O.C.T. the tissue samples can be positioned more easily in the microtome and have better qualities during sectioning.

Most cryosections are fixed using non-crosslinking agents. For isolation of RNA from tissue embedded in Tissue-Tek O.C.T. using non-crosslinking agents the RNeasy Plus Micro Kit or the RNeasy Micro Kit (Protocol: Total RNA Isolation from Microdissected Cryosections), or the RNeasy Mini Kit (RNeasy Mini Protocol for the isolation of Total RNA from Animal Tissue) give great results. We strongly recommend removing as much of the embedding compound as possible prior to RNA extraction from the sections. Please see QIAGEN News article, Issue 1 1998, 'Effects of malnutrition on expression of lactase in children' for successful RNA isolation from O.C.T.-embedded tissue using the RNeasy Mini Kit.

In case crosslinking agents (e.g. formaldehyde or glyoxal-containing) were used for fixation of the tissue for cryosectioning the RNeasy FFPE Kit is the perfect choice. The RNeasy FFPE Kit is especially designed for purifying total RNA from formalin-fixed tissue sections. Special lysis and incubation conditions reverse formaldehyde modification of RNA for improved results in downstream application. The crosslinking causes the RNA to break, resulting in overall smaller molecules, which look like a smear when analyzed on a formaldehyde gel.

In case DNA as well as RNA from precious samples is of interest from the identical sections, please have a look at the AllPrep DNA/RNA Kits for unfixed tissue or the AllPrep DNA/RNA FFPE Kit for fixed tissue.

FAQ ID -530
What is the minimum amount of starting material that can be used with the RNeasy Plus Micro and AllPrep DNA/RNA Micro Kit?

In our labs, we were able to purify RNA using the RNeasy Plus Micro Kit, or DNA/RNA using the AllPrep DNA/RNA Micro Kit at single cell level. However, generally we do not recommend purification from fewer than 10–20 cells, due to stochastics related to transcript copy numbers present in a single cell.

For example, if an RNA transcript is present at only 1 copy per cell, recovery from a purification using e.g., 10 cells or less, would be less than 1 transcript copy per microliter, given the recommended elution volume of 14 µl. 

FAQ ID -1750
Can tissue homogenized in Buffer RLT Plus instead of Buffer RLT be used with the AllPrep DNA/RNA/Protein Mini Kit?

No, Buffer APP for protein precipitation in the Allprep DNA/RNA/protein Mini Kit is not compatible with Buffer RLT Plus. Acetone can be used to precipitate proteins from samples homogenized in Buffer RLT Plus contained in the Allprep DNA/RNA Mini Kit and RNeasy Plus Mini Kit.  

 

FAQ ID -1577
Why does AllPrep DNA/RNA/Protein Mini kit use buffer RLT, but Allprep DNA/RNA Mini and Allprep DNA/RNA Micro kits use buffer RLT Plus? Are these buffers interchangeable?

Buffer RLT Plus contains detergents that are more ideal for binding of DNA to the AllPrep DNA mini spin columns.

But RLT Plus is not compatible with Buffer APP used to precipitate proteins in AllPrep DNA/RNA/Protein Mini kit. Therefore, we chose RLT instead of RLT Plus to get both DNA and proteins with this kit.

RLT lysates can also be used in AllPrep RNA/DNA kit or the AllPrep DNA/RNA Micro kit. DNA and RNA yields should be fine, but RNA may contain slightly higher levels of genomic DNA contamination.

FAQ ID - 3391
Can miRNA and other RNAs smaller than 200 nucleotides be isolated with the AllPrep DNA/RNA Micro Kit or RNeasy Plus Micro Kit?

Yes, RNAs smaller than 200 nucleotides, including miRNA, can be isolated using the AllPrep DNA/RNA Micro or RNeasy Plus Micro Kit. Please follow the specialized protocol 'Purification of total RNA containing small RNAs from cells' in Appendix D of the AllPrep DNA/RNA Micro or the RNeasy Plus Micro Handbook, respectively.

Please note that this protocol is for use with cultured cells only, and is not compatible with tissues.

 

FAQ ID -1749
What sample types can be used with the AllPrep DNA/RNA 96 Kit?

The Allprep DNA/RNA 96 kit is designed for cultured human or animal cells, and for easy-to-lyse human or animal tissues. Tissues compatible with RNeasy Mini, RNeasy Plus Mini, and RNeasy Plus 96 are also compatible with the Allprep DNA/RNA 96 kit.

For more information on compatible kits and sample types, see our Selection Guide for RNA purification.

FAQ ID -1996
Can DNase digestion be performed on the RNeasy 96 plate during the RNA purification part of the Allprep DNA/RNA 96 procedure?

In principle, it is possible. However, the efficiency of DNA binding to the AllPrep DNA 96 plate should be high enough so that no additional DNA removal/digestion is required.

 

FAQ ID -2000