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RNA Extraction from Tissue and Cells |
RNA extraction from tissues or cells begins with a process of lysing and denaturing cells to free up total nucleic acids. Whether you’re starting with cultured cells or tissue samples, or working with plants, bacteria, or mammalian cells, Thermo Fisher Scientific RNA extraction reagents and kits offer the right product for your research. The Thermo Fisher Scientific brand includes legacy Invitrogen products such as trusted TRIzol Reagents and PureLink purification kits, alongside premier products such as Cells-to-CT, MagMAX, and RNAlaterkits and reagents.
Store and stabilize RNA samples
RNAlater Solution is widely used for the preservation of RNA in intact animal tissues, organs, cells, and bacteria. It eliminates the need to immediately process samples for RNA isolation or to freeze them in liquid nitrogen for later processing.
RNA extraction from tissue samples
RNA extraction from tissue samples involves the isolation and purification of RNA molecules from a specific tissue. This method requires the retrieval of the tissue sample, which can be obtained through various techniques such as biopsies or surgical procedures. The tissue is then homogenized to disrupt the cells and release the RNA. The extracted RNA may contain a mixture of different cell types present in the tissue, which can introduce variability in the RNA composition. Therefore, it is crucial to carefully select the type and size of the tissue sample to help ensure the representation of the desired cell population.
Selection guide: Kits for RNA isolation from tissue
| Order now | Order now | Order now | Order now | Order now | Order now | Order now | |
| Gold standard for highly pure, intact RNA | Simple, reliable, rapid method | Fast and convenient column based, filter plate format for 96 samples (RNA >200 nt) | Fast and convenient column based method from limited sample input (RNA >200 nt) | Fast and convenient method for small RNA species | Highest purity TRIzol + column purification, no precipitation required | HTP format, capable of recovering RNA of all sizes (including microRNAs) | |
|---|---|---|---|---|---|---|---|
| TRIzol Reagent | PureLink RNA Mini Kit | PureLink Pro 96 total RNA Purification Kit | PureLink RNA Micro Scale Kit | mirVana miRNA Isolation Kit | TRIzol Plus RNA Purification System | MagMAX mirVana Total RNA Isolation | |
| Top seller | ✓ | ||||||
| Isolation method | High purity organic extraction (requires alcohol precipitation) | Fast, convenient silica column | Fast Convenient silica column in a filter plate format | Fast Convenient micro silica columns | Organic extraction combined with convenient silica columns | Highest purity and convenience; includes both organic extraction and silica column (no precipitation required) | Scalable, flexible format with magnetic beads |
| Prep time | 1 hour | 20 minutes | 20 minutes | 20 minutes | 30 minutes | 1 hour | <1 hour |
| Amount of starting material | Up to 100 mg | 10 mg to 100 mg | 10 cells to 10 mg | up to 10 mg | up to 250 mg tissue | Up to 100 mg | Up to 50 mg |
| High throughput compatible | ✓ | ✓ | |||||
| Prep size | 100 preps | 50 preps | 96 preps | 50 preps | 96 preps | 50 preps | 96 preps |
How to extract RNA from tissue?
- Collect the tissue sample and immediately snap-freeze it in liquid nitrogen or store it at –80°C for preservation.
- Grind the tissue sample to a fine powder using a pre-chilled mortar and pestle or homogenizer.
- Add Trizol or another RNA extraction reagent to the tube containing the tissue sample, following the recommended volume based on the sample size. Vortex vigorously to lyse the cells.
- Incubate the tube at room temperature for 5 minutes.
- Add chloroform to the tube in an equal volume. Shake vigorously for 15 seconds.
- Centrifuge the tube at high speed (12,000–16,000 x g) for 15 minutes at 4°C.
- Transfer the upper aqueous phase to a fresh tube, avoiding the interphase and organic phase.
- Add an equal volume of isopropanol to the tube and mix gently. Incubate at room temperature for 10 minutes.
- Centrifuge at high speed for 10 minutes at 4°C to pellet the RNA.
- Remove the supernatant, wash the RNA pellet with 75% ethanol, and centrifuge again for 5 minutes at 4°C.
- Remove the ethanol, air-dry the RNA pellet briefly, and dissolve it in RNase-free water or an appropriate buffer. Option to treat the RNA sample at this step with DNase I to remove genomic DNA contamination.
- Add an RNase inhibitor to protect the RNA from degradation and store the RNA sample at –80°C or use it for downstream applications.
Note: This protocol provides a basic overview of the RNA extraction process from tissue using Trizol or a similar reagent. It is important to refer to the specific instructions provided with the reagents for detailed guidelines and safety precautions.
Resources for RNA extraction from tissue
RNA extraction from cells
RNA extraction from cells is the process of isolating RNA specifically from cultured cells or cell suspensions. This method involves the enzymatic digestion of the cell membrane to release the cellular contents, including RNA. Unlike tissue samples, cell cultures provide a more homogeneous population of cells, allowing for a more specific analysis of gene expression within that population. Additionally, cell cultures can be manipulated and treated under controlled conditions, helping make it easier to study the effects of various experimental interventions on RNA expression.
From cells to qPCR results in minutes with Cells-to-CT kits
You can also analyze cultured cell lysates without first isolating the RNA. In significantly less time, you’ll get qPCR results equivalent to—or in some cases better than—those from purified RNA. The Invitrogen products such as Cells-to-CT and Single Cell-to-CT product lines offer tremendous performance and handling advantages.
Can RNA be extracted from cells?
Yes, RNA can be extracted from cells. The process is slightly different compared to extracting RNA from tissue samples because cultured cells are usually a homogenous population of cells and tissue is more heterogeneous, containing many cell populations and extracellular matrix.
RNA isolation from cell culture selection guide
| Order now | Order now | Order now | Order now | Order now | Order now | |
| Highly pure, intact RNA | Fast and convenient column based format for RNA (>200 nt) | Fast and convenient column based, filter plate format for 96 samples (RNA >200 nt) | Fast and convenient column based method from limited sample input (RNA >200 nt) | Fast and convenient method for small RNA species | Complete system for cells to qRT-PCR without RNA purification | |
|---|---|---|---|---|---|---|
| TRIzol Reagent | PureLink RNA Mini Kit | PureLink Pro 96 total RNA Purification Kit | PureLink RNA Micro Scale Kit | MirVana miRNA Isolation Kit | Cells-to-CT kits | |
| Top seller | ✓ | ✓ | ✓ | ✓ | ||
| Prep time | 1 hour | 20 minutes | 20 minutes | 20 minutes | 30 minutes | <10 minutes |
| Cell lysis method | High purity organic extraction (requires alcohol precipitation) | Nontoxic guanidine-isothiocyanate lysis | Nontoxic guanidine-isothiocyanate lysis | Nontoxic guanidine-isothiocyanate lysis | Organic extraction followed by alcohol precipitation | Cells-to-CT lysis |
| Amount of Starting material | Up to 1x107 cells | 5x106 to 1x108 cells | 5x106 to 1x108 cells | Up to 5x105 cells | 102–107 cultured cells | 10–100,000 cells |
| Application | All RNA expression methods | qRT-PCR, NGS | qRT-PCR, NGS | qRT-PCR, NGS | Micro RNA analysis | qRT-PCR |
Resources for RNA isolation from cell culture
FFPE RNA extraction
Extracting RNA from formalin-fixed paraffin-embedded (FFPE) samples is an important technique in molecular biology research. FFPE samples are commonly used in clinical and pathological studies, as they provide valuable archived tissue specimens. However, the preservation process of FFPE samples can cause significant degradation and cross-linking of RNA, making the extraction process challenging.
The method of extracting RNA from FFPE samples involves several key steps.
- First, the FFPE tissue section is deparaffinized by removing the paraffin wax using organic solvents.
- Next, the tissue is rehydrated and treated with proteinase K to digest proteins and reverse the cross-linking.
- This is followed by RNA extraction using various methods, such as column-based purification or phenol-chloroform extraction.
- Finally, the extracted RNA is assessed for quality and quantity using techniques like spectrophotometry or electrophoresis.
Due to the possibility of degradation and cross-linking of RNA in FFPE samples, the extracted RNA may not be of the highest quality. Therefore, it is essential to carefully evaluate the RNA integrity and consider using methods that are specifically designed for degraded RNA, such as RT-qPCR or RNA sequencing.
There are several factors that can impact the overall quality and yield of RNA isolated from FFPE tissues. Here is a summary of recommendations when working with FFPE samples:
- Upstream tissue procurement and tissue specimen preparation—If possible, tissues should be fixed within one hour of surgical resection. Extensive degradation of RNA can occur before completion of the fixation process. The optimal fixation time is 12–24 hours, using neutral-buffered formalin or paraformaldehyde. Fixed tissues should be thoroughly dehydrated prior to the embedding process.
- Block storage—Storage of blocks without cut faces, when possible, prevents ongoing damage from exposure to atmospheric oxygen, water, and other environmental factors such as light and infestation (fungus, insects, etc.).
- Tissue type, size, and amount being used for RNA isolation—The recommended tissue thickness is 10–20 µm. The number of sections used is determined by the tissue type (which impacts cell density) and surface area (recommended size: 50–300 mm2). Excess starting material can cause filter clogging, resulting in poor yield.
- Excessive amount of paraffin used for embedding tissues—When possible, excess paraffin should be trimmed away prior to starting the purification protocol. For xylene-based purification methods, two xylene treatments at room temperature should be sufficient for complete deparaffinization. If desired, a more rigorous 37–55°C treatment can be performed for up to 30 minutes. After the xylene deparaffinization, it is crucial that the 100% ethanol is completely removed, and the pellets are dry after the two 100% ethanol washes. The magnetic bead method employs novel chemistries to deal with the paraffin that limits input to 20 µm sections.
FFPE RNA isolation kit selection guide
| Order now | Order now | |
| Low-throughput isolation of RNA and DNA from the same FFPE section | Scalable isolation of RNA and DNA from the same FFPE section | |
|---|---|---|
| RecoverAll Total Nucleic Acid Isolation Kit for FFPE | MagMAX FFPE DNA/RNA Ultra Kit | |
| Prep Time | 4.5 hours (total time for 16 samples) 2.5 hrs hands-on time | 4 hours (total time for 96 preps) 1 hr hands-on time |
| Final product extracted | Total RNA, microRNA, gDNA | Total RNA, microRNA, gDNA |
| Isolation method | Column purification | Magnetic bead purification |
| Deparaffinization required | ✓ | ✓ |
| Automation compatible (post Deparaffinization) | ✓ (Scripts for KF Flex and Duo Prime) | |
| Compatible FFPE sample range | Up to 4 x 20 micron sections (300 mm2 tissue) | Up to 2 x 20 micron sections (300 mm2 tissue) |
| Sample volume | ~50 µL purified DNA ~50 µL purified RNA | ~50 uL purified DNA ~50 µL purified RNA |
| Compatible with Ion AmpliSeq DNA panels (e.g., Cancer Hotspot Panel v2) | ✓ | ✓ |
| Compatible with Ion AmpliSeq RNA panels (e.g., RNA cancer and RNA fusion) | ✓ | ✓ |
FFPE RNA extraction resources
Plant RNA extraction kits
Plant RNA extraction involves several key steps, including homogenization of the tissue to disrupt cell walls, treatment with extraction reagents to solubilize the cellular components, removal of contaminants, and purification of the extracted RNA. The method of extracting RNA from plant samples presents unique challenges due to the presence of rigid cell walls and high levels of secondary metabolites.
Plant RNA Isolation Aid for purification of total RNA from plant samples
One of the major issues with plant RNA isolation is the presence of problematic biomolecules, such as polyphenolic compounds and polysaccharides. The Invitrogen Plant RNA Isolation Aid minimizes many of these contaminants with the addition of polyvinylpyrrolidone, a high molecular weight polymer that binds to polyphenolics and polysaccharides and a pre-extraction spin step.
Plant RNA extraction kit selection guide
| Order now | Order now | Order now | Order now | |
| Great for difficult samples (conifer tissue & seeds) | Quick & easy to use | Efficient recovery of microRNA & small RNA | Rapid & fully automated | |
|---|---|---|---|---|
| Plant RNA Reagent | PureLink RNA Mini Kit | mirVana miRNA Isolation Kit | MagMAX-96 Total RNA Isolation Kit | |
| Top seller | ✓ | |||
| RNA types isolated | large RNA molecules only | large RNA molecules only | Small & large RNA molecules | large RNA molecules only |
| Prep time | 60 minutes | <20 minutes | 30 minutes | <45 minutes |
| Amount of starting material | Up to 1 g | <250 mg | 0.5 to 250 mg | Up to 10 mg |
| Isolation method | High purity organic extraction (requires alcohol precipitation) | Fast, convenient silica column | Highest purity & convenience; includes organic extraction & silica column (no precipitation required) | Scalable, flexible format with magnetic beads |
| High throughput compatible | ✓ |
Plant RNA isolation resources
Blood RNA extraction kits
Unlike cultured cells or tissue samples, extracting RNA from blood samples requires additional steps for cell separation and lysis to release the RNA from blood cells. Additionally, blood samples may contain various cell types, including red blood cells, platelets, and different subsets of white blood cells, which can introduce variability in the RNA composition. Therefore, careful consideration of the specific blood sample and appropriate protocols is necessary to help ensure successful RNA extraction.
RNA extraction from blood samples involves several key steps. First, the blood sample is collected and processed to separate the cellular fraction, which contains white blood cells, from the plasma or serum. The cellular fraction is then lysed to release the RNA, and the lysate is treated with reagents to stabilize and protect the RNA from degradation. RNA extraction kits utilize methods such as column-based purification or phenol-chloroform extraction to isolate the RNA from blood cells.
Blood RNA extraction kit selection guide
| Order now | Order now | Order now | Order now | Order now | Order now | |
| Feature | Optimized for liquid samples | Specialized kit deplete non-nucleated erythrocytes | Filter plate format with 96 columns, for HTP needs | HTP optimized for purification from stabilized blood samples | HTP format,capable of recovering RNA of all sizes (including microRNAs) | High RNA yield directly from whole blood, no need to isolate WBCs |
|---|---|---|---|---|---|---|
| TRIzol LS | PureLink Total RNA Blood Kit | PureLink Pro 96 total RNA Purification Kit | MagMAX for Stabilized Blood Tubes RNA Isolation Kit | MagMAX mirVana Total RNA Isolation | RiboPure Blood Kit | |
| Top seller | ✓ | |||||
| Compatible stabilization reagents | EDTA, Heparin, Citrate, RNAlater | EDTA, Heparin, Citrate | EDTA, Heparin, Citrate | Tempus or PaxGene tubes | EDTA or Citrate | EDTA, Heparin, Citrate, RNAlater |
| Stabilization reagent included | ✓ RNAlater | |||||
| Isolation method | High purity organic extraction (requires alcohol precipitation) | Fast, convenient silica column | Fast, convenient silica columns in a plate format | Scalable, flexible format with magnetic beads | Scalable, flexible format with magnetic beads | Highest purity & convenience; includes both organic extraction & silica column (no precipitation required) |
| Prep time | 1 hour | 20 minutes | 10-40 minutes | 12 tubes in 2 hours | 96 samples in <1 hr | 30 minutes |
| High throughput compatible | ✓ | ✓ | ✓ |
Blood collection tubes for RNA extraction
Tempus Blood RNA Tubes are available for the stabilization and purification of RNA from whole blood at the point of collection for downstream assays. Each Tempus tube contains a stabilizing and lysing reagent that eliminates the need for subsequent red blood cell lysis or proteinase K treatment. The RNA stabilizing reagent inactivates RNases and selectively precipitates RNA. Genomic DNA can also be isolated from the supernatant of the blood samples stored in a Tempus tube once the RNA is pelleted.
Resources for RNA isolation from blood
- Blood Fractionation Protocol for Collection of White Blood Cells
- Isolation of Small RNAs Using the RiboPure-Blood Kit
- Does Fractionation of Blood Samples Affect mRNA Expression Levels?
- Tips & Tricks for Working with Blood Samples
- Extract MicroRNA from Blood Samples
- High Throughput RNA Recovery from Mammalian, Plant, and Viral Samples
- Improve RNA Isolation for Array Analysis and More
- Improved Gene Expression Profiling with Mouse Blood Samples
- Improved Methods for Gene Expression Profiling from Blood Samples
- Improved Microarray Sensitivity using Whole Blood RNA Samples
- Isolate RNA from White Blood Cells Captured by a Novel Filter System
- Low and High Throughput RNA Isolation from Tissues, Cell-Free Samples, and Blood
- miRNA Expression in White Blood Cells
- Obtaining the Highest Quality RNA from Blood Samples
- Purify RNA Directly from Whole Blood
- Quantitate miRNA from a Few Drops of Mouse Blood
- Research Highlight: Superior Microarray Data from Blood Samples
- RNA Extraction from Blood: Choosing the Best System for Your Gene Expression Studies
- RNA from Mouse Whole Blood for Expression Profiling
- Robust High Throughput RNA Isolation from Blood Samples
- Superior Gene Expression Profiling with Human Whole Blood Samples
- Total RNA from Whole Blood for Expression Profiling
Isolation of RNA from yeast
Unlike cultured cells or tissue samples, extracting RNA from yeast samples is relatively straightforward due to the absence of complex cell structures, such as cell walls in plant cells or cell-cell junctions in animal tissues. Additionally, yeast samples typically contain a homogeneous population of cells, simplifying the extraction process and helping reduce variability in the RNA composition.
The method of extracting RNA from yeast samples involves three simple steps: 1) yeast cells are harvested and lysed to release the RNA via enzymatic digestion or mechanical disruption, 2) the lysate is treated with extraction reagents to solubilize cellular components and protect the RNA from degradation, and 3) RNA is extracted by column-based purification or phenol-chloroform extraction.
Yeast RNA isolation selection guide
| Order now | Order now | Order now | Order now | |
| Rapid & fully automated | Quick & easy to use | Designed for rigid yeast cell walls while maintaining expression profiles | Fast and convenient column based, filter plate format for 96 samples (RNA >200 nt) | |
|---|---|---|---|---|
| Platinum Taq MagMAX for Microarrays Total RNA Isolation Kit | PureLink RNA Mini Kit | RiboPure-Yeast Kit | PureLink Pro 96 total RNA Purification Kit | |
| Top seller | ✓ | |||
| Includes specialized beads for cell lysis | No | No | Zirconia beads | No |
| Isolation method | Scalable, flexible format for highest purity; includes organic extraction and magnetic beads | Fast, convenient silica column | Highest purity and convenience; includes both organic extraction and silica column | Fast, convenient silica column in 96 well filter plate format |
| Prep time | <1 hour | 20 minutes | 90 minutes (includes DNase treatment) | 20 minutes |
| Amount of starting material | Up to 5x106 cells | Up to 5x108 cells | Up to 3x108 cells | 1.8 mL of fresh, log-phase yeast cells (OD660=0.6–0.8) |
| High throughput compatible | ✓ | |||
| Kit size | 96 preps | 50 preps | 50 preps | 96 preps |
Yeast RNA isolation resources
Bacterial RNA extraction
Extracting RNA from bacteria samples is relatively straightforward compared to cultured cells or tissue samples due to the absence of complex cell structures. Bacteria samples typically contain a homogeneous population of cells, simplifying the RNA extraction process and helping reduce variability in RNA composition. Additionally, bacterial samples may require additional steps, such as enzymatic treatments to remove contaminating DNA, and obtain pure RNA samples.
Similar to RNA isolation in yeast samples, the method of extracting RNA from bacteria samples involves three simple steps: 1) bacterial cells are harvested and lysed to release the RNA via enzymatic digestion, mechanical disruption, or chemical lysis, 2) the lysate is treated with extraction reagents to solubilize cellular components and protect the RNA from degradation, and 3) RNA is extracted by column-based purification or phenol-chloroform extraction.
Selection guide: Bacterial RNA extraction kits
| Order now | Order now | Order now | Order now | |
| No lysis procedures | Fast & easy protocol, 20 min | Fast and convenient silica column based, filter plate format | HTP-compatible, 45 min | |
|---|---|---|---|---|
| TRIzol Max Bacterial RNA Isolation Kit | PureLink RNA Mini Kit | PureLink Pro 96 total RNA Purification Kit | MagMAX Total Nucleic Acid Isolation Kit | |
| Top seller | ✓ | |||
| Includes specialized beads for cell lysis | No | No | No | Zirconia beads |
| Isolation method | High purity organic extraction (requires alcohol precipitation) | Fast, convenient silica column | Fast, convenient silica column in 96 well filter plate format | Scalable, flexible format with magnetic beads |
| Prep time | 1 hour | 20 minutes | 20 minutes | 45 minutes |
| Amount of starting material | Up to 1x108 cells | Up to 1x109 cells | Up to 1x109 cells | Up to 0.3 g solid samples or 175 µL liquid samples |
| High throughput compatible | ✓ | ✓ | ||
| Kit size | 100 preps | 50 preps | 96 preps | 100 preps |
Bacterial RNA isolation resources
RNA extraction from tissue samples
RNA extraction from tissue samples involves the isolation and purification of RNA molecules from a specific tissue. This method requires the retrieval of the tissue sample, which can be obtained through various techniques such as biopsies or surgical procedures. The tissue is then homogenized to disrupt the cells and release the RNA. The extracted RNA may contain a mixture of different cell types present in the tissue, which can introduce variability in the RNA composition. Therefore, it is crucial to carefully select the type and size of the tissue sample to help ensure the representation of the desired cell population.
Selection guide: Kits for RNA isolation from tissue
| Order now | Order now | Order now | Order now | Order now | Order now | Order now | |
| Gold standard for highly pure, intact RNA | Simple, reliable, rapid method | Fast and convenient column based, filter plate format for 96 samples (RNA >200 nt) | Fast and convenient column based method from limited sample input (RNA >200 nt) | Fast and convenient method for small RNA species | Highest purity TRIzol + column purification, no precipitation required | HTP format, capable of recovering RNA of all sizes (including microRNAs) | |
|---|---|---|---|---|---|---|---|
| TRIzol Reagent | PureLink RNA Mini Kit | PureLink Pro 96 total RNA Purification Kit | PureLink RNA Micro Scale Kit | mirVana miRNA Isolation Kit | TRIzol Plus RNA Purification System | MagMAX mirVana Total RNA Isolation | |
| Top seller | ✓ | ||||||
| Isolation method | High purity organic extraction (requires alcohol precipitation) | Fast, convenient silica column | Fast Convenient silica column in a filter plate format | Fast Convenient micro silica columns | Organic extraction combined with convenient silica columns | Highest purity and convenience; includes both organic extraction and silica column (no precipitation required) | Scalable, flexible format with magnetic beads |
| Prep time | 1 hour | 20 minutes | 20 minutes | 20 minutes | 30 minutes | 1 hour | <1 hour |
| Amount of starting material | Up to 100 mg | 10 mg to 100 mg | 10 cells to 10 mg | up to 10 mg | up to 250 mg tissue | Up to 100 mg | Up to 50 mg |
| High throughput compatible | ✓ | ✓ | |||||
| Prep size | 100 preps | 50 preps | 96 preps | 50 preps | 96 preps | 50 preps | 96 preps |
How to extract RNA from tissue?
- Collect the tissue sample and immediately snap-freeze it in liquid nitrogen or store it at –80°C for preservation.
- Grind the tissue sample to a fine powder using a pre-chilled mortar and pestle or homogenizer.
- Add Trizol or another RNA extraction reagent to the tube containing the tissue sample, following the recommended volume based on the sample size. Vortex vigorously to lyse the cells.
- Incubate the tube at room temperature for 5 minutes.
- Add chloroform to the tube in an equal volume. Shake vigorously for 15 seconds.
- Centrifuge the tube at high speed (12,000–16,000 x g) for 15 minutes at 4°C.
- Transfer the upper aqueous phase to a fresh tube, avoiding the interphase and organic phase.
- Add an equal volume of isopropanol to the tube and mix gently. Incubate at room temperature for 10 minutes.
- Centrifuge at high speed for 10 minutes at 4°C to pellet the RNA.
- Remove the supernatant, wash the RNA pellet with 75% ethanol, and centrifuge again for 5 minutes at 4°C.
- Remove the ethanol, air-dry the RNA pellet briefly, and dissolve it in RNase-free water or an appropriate buffer. Option to treat the RNA sample at this step with DNase I to remove genomic DNA contamination.
- Add an RNase inhibitor to protect the RNA from degradation and store the RNA sample at –80°C or use it for downstream applications.
Note: This protocol provides a basic overview of the RNA extraction process from tissue using Trizol or a similar reagent. It is important to refer to the specific instructions provided with the reagents for detailed guidelines and safety precautions.
Resources for RNA extraction from tissue
RNA extraction from cells
RNA extraction from cells is the process of isolating RNA specifically from cultured cells or cell suspensions. This method involves the enzymatic digestion of the cell membrane to release the cellular contents, including RNA. Unlike tissue samples, cell cultures provide a more homogeneous population of cells, allowing for a more specific analysis of gene expression within that population. Additionally, cell cultures can be manipulated and treated under controlled conditions, helping make it easier to study the effects of various experimental interventions on RNA expression.
From cells to qPCR results in minutes with Cells-to-CT kits
You can also analyze cultured cell lysates without first isolating the RNA. In significantly less time, you’ll get qPCR results equivalent to—or in some cases better than—those from purified RNA. The Invitrogen products such as Cells-to-CT and Single Cell-to-CT product lines offer tremendous performance and handling advantages.
Can RNA be extracted from cells?
Yes, RNA can be extracted from cells. The process is slightly different compared to extracting RNA from tissue samples because cultured cells are usually a homogenous population of cells and tissue is more heterogeneous, containing many cell populations and extracellular matrix.
RNA isolation from cell culture selection guide
| Order now | Order now | Order now | Order now | Order now | Order now | |
| Highly pure, intact RNA | Fast and convenient column based format for RNA (>200 nt) | Fast and convenient column based, filter plate format for 96 samples (RNA >200 nt) | Fast and convenient column based method from limited sample input (RNA >200 nt) | Fast and convenient method for small RNA species | Complete system for cells to qRT-PCR without RNA purification | |
|---|---|---|---|---|---|---|
| TRIzol Reagent | PureLink RNA Mini Kit | PureLink Pro 96 total RNA Purification Kit | PureLink RNA Micro Scale Kit | MirVana miRNA Isolation Kit | Cells-to-CT kits | |
| Top seller | ✓ | ✓ | ✓ | ✓ | ||
| Prep time | 1 hour | 20 minutes | 20 minutes | 20 minutes | 30 minutes | <10 minutes |
| Cell lysis method | High purity organic extraction (requires alcohol precipitation) | Nontoxic guanidine-isothiocyanate lysis | Nontoxic guanidine-isothiocyanate lysis | Nontoxic guanidine-isothiocyanate lysis | Organic extraction followed by alcohol precipitation | Cells-to-CT lysis |
| Amount of Starting material | Up to 1x107 cells | 5x106 to 1x108 cells | 5x106 to 1x108 cells | Up to 5x105 cells | 102–107 cultured cells | 10–100,000 cells |
| Application | All RNA expression methods | qRT-PCR, NGS | qRT-PCR, NGS | qRT-PCR, NGS | Micro RNA analysis | qRT-PCR |
Resources for RNA isolation from cell culture
FFPE RNA extraction
Extracting RNA from formalin-fixed paraffin-embedded (FFPE) samples is an important technique in molecular biology research. FFPE samples are commonly used in clinical and pathological studies, as they provide valuable archived tissue specimens. However, the preservation process of FFPE samples can cause significant degradation and cross-linking of RNA, making the extraction process challenging.
The method of extracting RNA from FFPE samples involves several key steps.
- First, the FFPE tissue section is deparaffinized by removing the paraffin wax using organic solvents.
- Next, the tissue is rehydrated and treated with proteinase K to digest proteins and reverse the cross-linking.
- This is followed by RNA extraction using various methods, such as column-based purification or phenol-chloroform extraction.
- Finally, the extracted RNA is assessed for quality and quantity using techniques like spectrophotometry or electrophoresis.
Due to the possibility of degradation and cross-linking of RNA in FFPE samples, the extracted RNA may not be of the highest quality. Therefore, it is essential to carefully evaluate the RNA integrity and consider using methods that are specifically designed for degraded RNA, such as RT-qPCR or RNA sequencing.
There are several factors that can impact the overall quality and yield of RNA isolated from FFPE tissues. Here is a summary of recommendations when working with FFPE samples:
- Upstream tissue procurement and tissue specimen preparation—If possible, tissues should be fixed within one hour of surgical resection. Extensive degradation of RNA can occur before completion of the fixation process. The optimal fixation time is 12–24 hours, using neutral-buffered formalin or paraformaldehyde. Fixed tissues should be thoroughly dehydrated prior to the embedding process.
- Block storage—Storage of blocks without cut faces, when possible, prevents ongoing damage from exposure to atmospheric oxygen, water, and other environmental factors such as light and infestation (fungus, insects, etc.).
- Tissue type, size, and amount being used for RNA isolation—The recommended tissue thickness is 10–20 µm. The number of sections used is determined by the tissue type (which impacts cell density) and surface area (recommended size: 50–300 mm2). Excess starting material can cause filter clogging, resulting in poor yield.
- Excessive amount of paraffin used for embedding tissues—When possible, excess paraffin should be trimmed away prior to starting the purification protocol. For xylene-based purification methods, two xylene treatments at room temperature should be sufficient for complete deparaffinization. If desired, a more rigorous 37–55°C treatment can be performed for up to 30 minutes. After the xylene deparaffinization, it is crucial that the 100% ethanol is completely removed, and the pellets are dry after the two 100% ethanol washes. The magnetic bead method employs novel chemistries to deal with the paraffin that limits input to 20 µm sections.
FFPE RNA isolation kit selection guide
| Order now | Order now | |
| Low-throughput isolation of RNA and DNA from the same FFPE section | Scalable isolation of RNA and DNA from the same FFPE section | |
|---|---|---|
| RecoverAll Total Nucleic Acid Isolation Kit for FFPE | MagMAX FFPE DNA/RNA Ultra Kit | |
| Prep Time | 4.5 hours (total time for 16 samples) 2.5 hrs hands-on time | 4 hours (total time for 96 preps) 1 hr hands-on time |
| Final product extracted | Total RNA, microRNA, gDNA | Total RNA, microRNA, gDNA |
| Isolation method | Column purification | Magnetic bead purification |
| Deparaffinization required | ✓ | ✓ |
| Automation compatible (post Deparaffinization) | ✓ (Scripts for KF Flex and Duo Prime) | |
| Compatible FFPE sample range | Up to 4 x 20 micron sections (300 mm2 tissue) | Up to 2 x 20 micron sections (300 mm2 tissue) |
| Sample volume | ~50 µL purified DNA ~50 µL purified RNA | ~50 uL purified DNA ~50 µL purified RNA |
| Compatible with Ion AmpliSeq DNA panels (e.g., Cancer Hotspot Panel v2) | ✓ | ✓ |
| Compatible with Ion AmpliSeq RNA panels (e.g., RNA cancer and RNA fusion) | ✓ | ✓ |
FFPE RNA extraction resources
Plant RNA extraction kits
Plant RNA extraction involves several key steps, including homogenization of the tissue to disrupt cell walls, treatment with extraction reagents to solubilize the cellular components, removal of contaminants, and purification of the extracted RNA. The method of extracting RNA from plant samples presents unique challenges due to the presence of rigid cell walls and high levels of secondary metabolites.
Plant RNA Isolation Aid for purification of total RNA from plant samples
One of the major issues with plant RNA isolation is the presence of problematic biomolecules, such as polyphenolic compounds and polysaccharides. The Invitrogen Plant RNA Isolation Aid minimizes many of these contaminants with the addition of polyvinylpyrrolidone, a high molecular weight polymer that binds to polyphenolics and polysaccharides and a pre-extraction spin step.
Plant RNA extraction kit selection guide
| Order now | Order now | Order now | Order now | |
| Great for difficult samples (conifer tissue & seeds) | Quick & easy to use | Efficient recovery of microRNA & small RNA | Rapid & fully automated | |
|---|---|---|---|---|
| Plant RNA Reagent | PureLink RNA Mini Kit | mirVana miRNA Isolation Kit | MagMAX-96 Total RNA Isolation Kit | |
| Top seller | ✓ | |||
| RNA types isolated | large RNA molecules only | large RNA molecules only | Small & large RNA molecules | large RNA molecules only |
| Prep time | 60 minutes | <20 minutes | 30 minutes | <45 minutes |
| Amount of starting material | Up to 1 g | <250 mg | 0.5 to 250 mg | Up to 10 mg |
| Isolation method | High purity organic extraction (requires alcohol precipitation) | Fast, convenient silica column | Highest purity & convenience; includes organic extraction & silica column (no precipitation required) | Scalable, flexible format with magnetic beads |
| High throughput compatible | ✓ |
Plant RNA isolation resources
Blood RNA extraction kits
Unlike cultured cells or tissue samples, extracting RNA from blood samples requires additional steps for cell separation and lysis to release the RNA from blood cells. Additionally, blood samples may contain various cell types, including red blood cells, platelets, and different subsets of white blood cells, which can introduce variability in the RNA composition. Therefore, careful consideration of the specific blood sample and appropriate protocols is necessary to help ensure successful RNA extraction.
RNA extraction from blood samples involves several key steps. First, the blood sample is collected and processed to separate the cellular fraction, which contains white blood cells, from the plasma or serum. The cellular fraction is then lysed to release the RNA, and the lysate is treated with reagents to stabilize and protect the RNA from degradation. RNA extraction kits utilize methods such as column-based purification or phenol-chloroform extraction to isolate the RNA from blood cells.
Blood RNA extraction kit selection guide
| Order now | Order now | Order now | Order now | Order now | Order now | |
| Feature | Optimized for liquid samples | Specialized kit deplete non-nucleated erythrocytes | Filter plate format with 96 columns, for HTP needs | HTP optimized for purification from stabilized blood samples | HTP format,capable of recovering RNA of all sizes (including microRNAs) | High RNA yield directly from whole blood, no need to isolate WBCs |
|---|---|---|---|---|---|---|
| TRIzol LS | PureLink Total RNA Blood Kit | PureLink Pro 96 total RNA Purification Kit | MagMAX for Stabilized Blood Tubes RNA Isolation Kit | MagMAX mirVana Total RNA Isolation | RiboPure Blood Kit | |
| Top seller | ✓ | |||||
| Compatible stabilization reagents | EDTA, Heparin, Citrate, RNAlater | EDTA, Heparin, Citrate | EDTA, Heparin, Citrate | Tempus or PaxGene tubes | EDTA or Citrate | EDTA, Heparin, Citrate, RNAlater |
| Stabilization reagent included | ✓ RNAlater | |||||
| Isolation method | High purity organic extraction (requires alcohol precipitation) | Fast, convenient silica column | Fast, convenient silica columns in a plate format | Scalable, flexible format with magnetic beads | Scalable, flexible format with magnetic beads | Highest purity & convenience; includes both organic extraction & silica column (no precipitation required) |
| Prep time | 1 hour | 20 minutes | 10-40 minutes | 12 tubes in 2 hours | 96 samples in <1 hr | 30 minutes |
| High throughput compatible | ✓ | ✓ | ✓ |
Blood collection tubes for RNA extraction
Tempus Blood RNA Tubes are available for the stabilization and purification of RNA from whole blood at the point of collection for downstream assays. Each Tempus tube contains a stabilizing and lysing reagent that eliminates the need for subsequent red blood cell lysis or proteinase K treatment. The RNA stabilizing reagent inactivates RNases and selectively precipitates RNA. Genomic DNA can also be isolated from the supernatant of the blood samples stored in a Tempus tube once the RNA is pelleted.
Resources for RNA isolation from blood
- Blood Fractionation Protocol for Collection of White Blood Cells
- Isolation of Small RNAs Using the RiboPure-Blood Kit
- Does Fractionation of Blood Samples Affect mRNA Expression Levels?
- Tips & Tricks for Working with Blood Samples
- Extract MicroRNA from Blood Samples
- High Throughput RNA Recovery from Mammalian, Plant, and Viral Samples
- Improve RNA Isolation for Array Analysis and More
- Improved Gene Expression Profiling with Mouse Blood Samples
- Improved Methods for Gene Expression Profiling from Blood Samples
- Improved Microarray Sensitivity using Whole Blood RNA Samples
- Isolate RNA from White Blood Cells Captured by a Novel Filter System
- Low and High Throughput RNA Isolation from Tissues, Cell-Free Samples, and Blood
- miRNA Expression in White Blood Cells
- Obtaining the Highest Quality RNA from Blood Samples
- Purify RNA Directly from Whole Blood
- Quantitate miRNA from a Few Drops of Mouse Blood
- Research Highlight: Superior Microarray Data from Blood Samples
- RNA Extraction from Blood: Choosing the Best System for Your Gene Expression Studies
- RNA from Mouse Whole Blood for Expression Profiling
- Robust High Throughput RNA Isolation from Blood Samples
- Superior Gene Expression Profiling with Human Whole Blood Samples
- Total RNA from Whole Blood for Expression Profiling
Isolation of RNA from yeast
Unlike cultured cells or tissue samples, extracting RNA from yeast samples is relatively straightforward due to the absence of complex cell structures, such as cell walls in plant cells or cell-cell junctions in animal tissues. Additionally, yeast samples typically contain a homogeneous population of cells, simplifying the extraction process and helping reduce variability in the RNA composition.
The method of extracting RNA from yeast samples involves three simple steps: 1) yeast cells are harvested and lysed to release the RNA via enzymatic digestion or mechanical disruption, 2) the lysate is treated with extraction reagents to solubilize cellular components and protect the RNA from degradation, and 3) RNA is extracted by column-based purification or phenol-chloroform extraction.
Yeast RNA isolation selection guide
| Order now | Order now | Order now | Order now | |
| Rapid & fully automated | Quick & easy to use | Designed for rigid yeast cell walls while maintaining expression profiles | Fast and convenient column based, filter plate format for 96 samples (RNA >200 nt) | |
|---|---|---|---|---|
| Platinum Taq MagMAX for Microarrays Total RNA Isolation Kit | PureLink RNA Mini Kit | RiboPure-Yeast Kit | PureLink Pro 96 total RNA Purification Kit | |
| Top seller | ✓ | |||
| Includes specialized beads for cell lysis | No | No | Zirconia beads | No |
| Isolation method | Scalable, flexible format for highest purity; includes organic extraction and magnetic beads | Fast, convenient silica column | Highest purity and convenience; includes both organic extraction and silica column | Fast, convenient silica column in 96 well filter plate format |
| Prep time | <1 hour | 20 minutes | 90 minutes (includes DNase treatment) | 20 minutes |
| Amount of starting material | Up to 5x106 cells | Up to 5x108 cells | Up to 3x108 cells | 1.8 mL of fresh, log-phase yeast cells (OD660=0.6–0.8) |
| High throughput compatible | ✓ | |||
| Kit size | 96 preps | 50 preps | 50 preps | 96 preps |
Yeast RNA isolation resources
Bacterial RNA extraction
Extracting RNA from bacteria samples is relatively straightforward compared to cultured cells or tissue samples due to the absence of complex cell structures. Bacteria samples typically contain a homogeneous population of cells, simplifying the RNA extraction process and helping reduce variability in RNA composition. Additionally, bacterial samples may require additional steps, such as enzymatic treatments to remove contaminating DNA, and obtain pure RNA samples.
Similar to RNA isolation in yeast samples, the method of extracting RNA from bacteria samples involves three simple steps: 1) bacterial cells are harvested and lysed to release the RNA via enzymatic digestion, mechanical disruption, or chemical lysis, 2) the lysate is treated with extraction reagents to solubilize cellular components and protect the RNA from degradation, and 3) RNA is extracted by column-based purification or phenol-chloroform extraction.
Selection guide: Bacterial RNA extraction kits
| Order now | Order now | Order now | Order now | |
| No lysis procedures | Fast & easy protocol, 20 min | Fast and convenient silica column based, filter plate format | HTP-compatible, 45 min | |
|---|---|---|---|---|
| TRIzol Max Bacterial RNA Isolation Kit | PureLink RNA Mini Kit | PureLink Pro 96 total RNA Purification Kit | MagMAX Total Nucleic Acid Isolation Kit | |
| Top seller | ✓ | |||
| Includes specialized beads for cell lysis | No | No | No | Zirconia beads |
| Isolation method | High purity organic extraction (requires alcohol precipitation) | Fast, convenient silica column | Fast, convenient silica column in 96 well filter plate format | Scalable, flexible format with magnetic beads |
| Prep time | 1 hour | 20 minutes | 20 minutes | 45 minutes |
| Amount of starting material | Up to 1x108 cells | Up to 1x109 cells | Up to 1x109 cells | Up to 0.3 g solid samples or 175 µL liquid samples |
| High throughput compatible | ✓ | ✓ | ||
| Kit size | 100 preps | 50 preps | 96 preps | 100 preps |
Bacterial RNA isolation resources
Protect your RNA and keep it safe
Resources
Nucleic Acid Purification and Analysis Support Center
Find tips, troubleshooting help, and resources for your nucleic acid purification & analysis applications.
- Protocol Videos—Videos to help you isolate nucleic acids using a variety of techniques.
- DNA & RNA Selection Guide—Find the right purification products.
- Videos—View our library of DNA & RNA purification and analysis videos.
- Application Notes—Explore our application notes from scientists sharing data for isolation products
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