Sample Technologies

Innovative technologies deliver high yields of high-quality nucleic acids
High quality starting material is essential for reliable next-generation sequencing results and accurate data analysis. QIAGEN, with leading expertise in sample preparation technologies, offers solutions that deliver high yields of superior-quality nucleic acids and enable outstanding results — on any sequencing platform.

QIAGEN's wide range of sample technologies delivers:
  • High-quality DNA and RNA purification, even from challenging sample types
  • Unbiased whole genome amplification from a single cell
  • Time savings and standardization with automated purification
DNAseq NGS workflow
DNA purification from challenging samples
Unbiased whole genome amplification from single cells and limited sample material

RNAseq NGS workflow
High-quality RNA purification

Automation for all NGS workflows
Automated sample purification on the QIAcube
Sample purification is a critical step for obtaining accurate NGS data (see figure DNA purity depends on the isolation method). Even the best and most robust NGS technologies can only provide reliable results if the template nucleic acid is of adequate quality and purity. QIAGEN’s diverse portfolio of sample prep solutions is especially adapted to overcome all challenges in DNA and RNA purification, including low yields, poor quality, and difficult sample types, such as formalin-fixed, paraffin-embedded (FFPE) samples (see table "Wide range of purification kits). All QIAGEN NGS sample prep solutions can be easily automated on the QIAcube, ensuring greater standardization and time savings.

Wide range of purification kits
Sample type Nucleic acid  Kit
Plant cells or tissues  DNA DNeasy Plant Mini Kit
Blood  DNA QIAamp DNA Blood Mini Kit
Tissues, swabs, CSF, blood, body fluids  DNA QIAamp DNA Mini Kit
High-molecular-weight DNA  DNA MagAttract HMW DNA Kit
Cells, easy-to-lyse tissues, plant  RNA RNeasy Plus Kits
All types of difficult to lyse tissues  RNA RNeasy Plus Universal Kits
FFPE tissue  RNA RNeasy FFPE Kit

DNAseq NGS workflow
High-quality DNA purification — even from challenging sample types
For use with all sample types, QIAamp and DNeasy Kits deliver consistent, high yields of DNA with complete removal of contaminants and inhibitors (see table "Yields with the QIAamp DNA Mini Kit"). Purified DNA is up to 50 kb, making it highly suited for long-range PCR amplification and NGS applications (see figure Efficient long-range PCR and Purified genomic DNA up to 50 kb).

Yields with the QIAamp DNA Mini Kit
 Yield
Sample  Starting amount  Total nucleic acids (µg) DNA (µg)
 Blood  (200 µl)  4–12   4–12
 Buffy coat  (200 µl)  25–50  25–50
 Cells  (107)  40–60  30–40
 Liver  (25 mg)  60–115  10–30
 Brain  (25 mg)  35–60  15–30
 Lung  (25 mg)  25–45   5–10
 Heart  (25 mg)  15–40   5–10
 Kidney  (25 mg)  40–85  15–30
 Spleen  (10 mg)  25–45   5–30
  Nucleic acids obtained without RNase treatment.
  Nucleic acids obtained with RNase treatment.

Purification of high-molecular-weight DNA
For sensitive applications like NGS, it is essential that inhibitors, such as anticoagulants, enzymes, and divalent cations, are completely eliminated from purified DNA. The MagAttract HMW DNA Kit successfully isolates high-molecular-weight (HMW) DNA (100–200 kb) using a simple, magnetic bead-based protocol, and delivers high yields of DNA that is especially suited for NGS applications (see figure Successful isolation of high-molecular-weight DNA). Real-time PCR amplification of DNA using the MagAttract HMW DNA Kit demonstrates the complete lack of inhibition in all samples (see figure No inhibition in samples derived from anti-coagulated blood).

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Unbiased whole genome amplification from single cells and limited sample material, recommended for use in NGS
The REPLI-g Single Cell Kit uniformly amplifies gDNA from single cells without purification (<1000 cells to as little as 1 bacterial or tumor cell) or purified gDNA. Negligible sequence bias and maximized genome coverage make the REPLI-g Single Cell Kit an excellent tool for a wide range of NGS applications, including cancer research, metagenomics, and stem cell biology.

DNA sequence analysis of biological samples using innovative instrumentation, such as next-generation sequencing platforms,  is often limited by the small amount of sample available. DNA amplified using the REPLI-g Single Cell Kit has been tested with, and is highly suited for, numerous downstream analyses, including NGS. Since there is no requirement for a separate PCR-based amplification step, REPLI-g whole genome amplification and library preparation requires less hands-on time and results in longer read-lengths than PCR-based methods (see figure Less hands-on time and more sequence information). High-quality, comparable NGS results showing a high percentage of sequence coverage and very low error rates are achieved with both purified genomic DNA or REPLI-g Single Cell amplified DNA, including when starting from just a single bacterial cell (see figure Comparable NGS results). These findings are underscored by a comprehensive analysis of a wide range of markers covering all human autosomal chromosomes and the X chromosome, with 3 different independent experiments demonstrating that DNA is successfully amplified from all areas of the genome without a single drop-out (see figure Complete genome coverage). Unlike with the REPLI-g Single Cell Kit, single cells analyzed using kits from other suppliers often fail in complete and unbiased sequence representation (see figure Unbiased DNA amplification from a single cell).

Unbiased amplification from a single cell is achieved with Multiple Displacement Amplification (MDA) technology and a modified form of Phi 29 Polymerase (see figure Multiple Displacement Amplification (MDA) technology, along with a unique, controlled decontamination procedure to avoid amplification of contaminating DNA, ensuring highly reliable results each time (see figure Innovative UV treatment). For more detailed information on REPLI-g whole genome amplification, see our WGA spotlight page.

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RNAseq NGS workflow
High-quality RNA purification
Purification of high-quality RNA can be challenging due to rapid degradation, and is an important consideration in your RNAseq workflow. RNeasy is the standard technology for high-quality RNA purification. RNeasy Plus Kits integrate fast, convenient RNA purification with effective elimination of genomic DNA (gDNA), while RNeasy Plus Universal Kits are especially suited for difficult-to-lyse tissues. High, reproducible RNA yields are achieved from a wide range of sample materials (see table "Typical yields of total RNA with RNeasy Plus Universal Kits").

Typical yields of total RNA with RNeasy Plus Universal Kits
Mouse/rat tissue (10 mg) Yield of total RNA (µg)*
 Adipose tissue  0.5–2.5
 Brain  5–20
 Heart  5–25
 Intestine  10–60
 Kidney  5–40
 Liver  15–80
 Lung  5–15
 Muscle  5–35
 Skin  2–5
 Spleen  15–100
* Yields can vary due to factors such as species and experimental stage.

Analysis of purified RNA using the QIAxcel system demonstrates excellent RNA integrity (see figure High-quality RNA). gDNA Eliminator Solution and RNeasy technologies efficiently remove most gDNA contamination without DNase treatment (see figure Effective removal of genomic DNA).

RNeasy Plus Kits, in combination with the GeneRead rRNA Depletion Kit, deliver highly pure RNA that is especially suited for NGS applications — with more than 99.5% of rRNA depleted from the sample (see figure Highly efficient rRNA removal).

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Automation for all NGS workflows
Save time and standardize your NGS results with automated sample purification on the QIAcube
The innovative QIAcube uses advanced technology to process QIAGEN spin columns, enabling seamless integration of automated, low-throughput sample prep into your laboratory workflow. No change of purification chemistry is required, assuring fast startup and immediate results. All steps in the purification procedure are fully automated — and up to 12 samples can be processed per run. The QIAcube fully automates more than 40 QIAGEN spin-column kits using a simple lyse, bind, wash, elute procedure and is an important component of the GeneReader Sample to Insight workflow.


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For isolation of high-molecular-weight genomic DNA
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REPLI-g Single Cell Kit (24)
For highly uniform whole genome amplification (WGA) from single cells or limited sample material
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For purification of total RNA from all types of tissue using gDNA Eliminator Solution
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For purification of up to 12 µg genomic, mitochondrial, or viral DNA from blood and related body fluids
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For isolation of up to 30 µg total cellular DNA from plant cells and tissues, or fungi
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No inhibition in samples derived from anti-coagulated blood.
No inhibition in samples derived from anti-coagulated blood.
[A] and [B] Samples were processed with the MagAttract HMW DNA Kit. Different volumes of eluate were used as indicated. Variables CT values from sample to sample are the results of WBC content variations.
Comparable NGS results using genomic or single-cell amplified DNA
Comparable NGS results obtained using purified genomic DNA or REPLI-g Single Cell amplified DNA.
Whole genome sequencing of the Bacillus subtilis genome was performed on the Illumina MiSeq instrument. For analysis, 2 μg of genomic DNA or DNA amplified from a single cell (three different single cell experiments) and 103 cells, using the REPLI-g Single Cell Kit, was sheared into 300 bp fragments and 1 μg of each was used for library preparation. Comparable sequence coverage was observed for gDNA and REPLI-g Single Cell amplified DNA*. Comparison of nonamplified and REPLI-g amplified DNA revealed error rates in a similar, very low, percentage range.
* Aligned using the Burrows-Wheeler Alignment program (cut-off: 10x coverage): bio-bwa.sourceforge.net.
Comparison on non-amplified and REPLI-g Single Cell amplified DNA also revealed that sequences mapped to the genome with high percentage rates (data not shown
Complete genome coverage.
Complete genome coverage.
Comprehensive analysis of 267 loci spread out over different chromosomes across the entire human genome (as indicated) was performed using RT2 qPCR Primer Assays (QIAGEN) and real-time PCR following DNA amplification with the REPLI-g Single Cell Kit from 3 different single cell experiments. Low and consistent CT values, with no dropout from any marker, indicate that DNA was successfully amplified from all areas of the genome and is highly suited for single-cell genomics.
DNA Purity Depends on Isolation Method
DNA purity depends on the isolation method.
Spectrophotometric scans (220–320 nm) of DNA isolated from leaves/needles using the method of Dellaporta (1), CTAB (2), or the DNeasy Plant Mini Kit. Pure DNA typically shows a symmetrical peak at 260 nm and a smooth profile. Polysaccharides and other secondary metabolites, often copurified with plant DNA isolated using traditional methods, can interfere with OD readings (A260/A280), leading to errors in determination of concentration and purity.
Effective removal of genomic DNA.
Effective removal of genomic DNA.
RNA was isolated from the indicated amounts of RNAlater stabilized rat kidney using the RNeasy Plus Universal Mini Kit or was precipitated using a precipitation reagent from Supplier AII. RNA eluates were analyzed by real-time PCR, with and without reverse transcription, using the QuantiFast Probe RT-PCR Kit and the Rotor-Gene Q.
Efficient long-range PCR
Efficient long-range PCR.
Amplification of a 10 kb fragment of the human ALDH1 gene from genomic DNA isolated from blood. DNA was purified using conventional methods (Phenol) or the QIAamp DNA Blood Maxi Kit (QIAamp). M: 1 kb ladder.
Successful isolation of high-molecular-weight DNA.
Successful isolation of high-molecular-weight DNA.
DNA was isolated from 200 µl of blood stabilized with EDTA, citrate, and heparin respectively, using the standard method recommended for each procedure. The MagAttract HMW DNA Kit outperformed products from other suppliers and enabled successful isolation of 200 kb high-molecular-weight DNA. M: Marker.
Highly efficient rRNA removal
Highly efficient rRNA removal.
[A] The lack of any rRNA peak in QIAxcel trace data demonstrates complete removal of rRNA in the rRNA-depleted sample, in contrast to the total RNA sample. [B] qRT-PCR assays indicate that more than 99% of all rRNA species, including mitochondrial rRNA, are removed with the kit.
High-quality RNA
High-quality RNA.
RNA was purified from rat tissue using the RNeasy Plus Universal Mini Kit with or without gDNA Eliminator Solution. [A] Real-time RT-PCR analysis was carried out using RNA isolated from 25 mg frozen liver tissue. The CT value of all samples was comparable. DNA contamination was detected in the -RT control if gDNA Eliminator Solution was not used, whereas the samples isolated using gDNA Eliminator Solution showed minor or no DNA contamination. [B] RNA was purified from 25 mg stabilized heart tissues. Data obtained using the QIAxcel system demonstrates good RNA integrity regardless of whether RNA was isolated using gDNA Eliminator Solution.
Innovative UV treatment eliminates any detectable trace of residual DNA in kit components
Innovative UV treatment.
Bacterial DNA (2000 copies) was spiked into REPLI-g sc Reaction Buffer, which was then irradiated with UV using the standard procedure for all buffers and reagents provided with the REPLI-g Single Cell Kit (following UV treatment, the kits undergo stringent quality control to ensure complete functionality). In subsequent real-time PCR, no bacterial DNA was detectable following the UV decontamination procedure.
Next-generation sequencing using REPLI-g amplified DNA requires less hands-on time and generates more sequence information than PCR-based methods
Less hands-on time and more sequence information.
PCR-based whole genome amplification (WGA) and library preparation for next-generation sequencing requires a purification step prior to library preparation that can result in ~3 times more hands-on time than REPLI-g based WGA and library preparation. Additionally, unlike REPLI-g amplified DNA, PCR-based methods also include PCR primer binding sites (indicated in red) on the WGA amplification product. Since next-generation sequencing read-lengths are between 50–200 bp, the resulting genome coverage could be strongly reduced using a PCR-based WGA method.
Multiple Displacement Amplification (MDA) technology delivers long read lengths with isothermal amplification.
Multiple Displacement Amplification (MDA) technology delivers long read lengths with isothermal amplification.
Primers (arrows) anneal to the template DNA and are extended at 30°C by Phi 29 polymerase, which moves along the DNA template strand, displacing the complementary strand while becoming a template itself for replication. In contrast to PCR amplification, MDA does not require different temperatures and ends in very long fragments with low mutation rates.
Purified Genomic DNA up to 50 kb  Size distribution of DNA prepared with QIAamp Kits from the indicated sources (3 µg per lane)
Purified genomic DNA up to 50 kb.
Size distribution of DNA prepared with QIAamp Kits from the indicated sources (3 µg per lane).
Automate your NGS purification.
The innovative QIAcube uses advanced technology to process QIAGEN spin columns, enabling seamless integration of automated sample preparation into your NGS workflow.
The REPLI-g Single Cell Kit delivers unbiased amplification of DNA from a single cell
The REPLI-g Single Cell Kit delivers highly reliable, unbiased amplification of DNA from a single cell.
The REPLI-g Single Cell Kit or single cell kits from Suppliers G, N, and S were used to individually amplify 5 human cells. Real-time PCR was used to analyze 3 markers to identify loss or variability in the amount of genomic loci. Unlike kits from other suppliers, the REPLI-g Single Cell Kit delivered unbiased amplification of DNA in each of the 5 cells, indicated by equivalent CT values for each marker. Unlike with the REPLI-g Single Cell Kit, DNA amplified using the kits from Suppliers G and N demonstrated high dropout rates. For both kits, genomic marker X54 was not amplified in 2 of the 5 cells tested, and the kit from Supplier G did not amplify marker 99 in 1 of the 5 cells, indicating incomplete genome coverage and biased amplification that makes these kits unsuitable for reliable single cell research.