Gene-expression-analysis

Gene expression analysis is a real-time PCR application that plays a critical role in various SARS-CoV-2 research areas, from basic research to future vaccine and therapeutic development. Identifying key gene expression pathways and networks are crucial to understanding coronavirus pathogenesis, tropism, and transmission.

Gene expression analysis requires high-quality RNA for real-time RT-PCR. Select the RNA isolation method that is best suited to your sample type and throughput needs.

Learn more ›

TaqMan Gene Expression Assay selection

Our Applied Biosystem TaqMan Gene Expression Assays consist of target primers and an optimized sequence-specific probe (with no extra design, optimization, or melt-curve analysis needed). Explore predesigned assays for the curated list of genes associated with SARS-CoV-2 viral and host target research below, or search our database of more than 2.3 million gene expression assays for additional targets of interest. TaqMan Assays are available in four format options  to meet your experiment through-put needs: single-tube, 96-well plates (0.1 and 0.2 mL), TaqMan Array Cards or OpenArray plates. For simultaneous interrogation of multiple genes related to in SARS-CoV-2 infection and pathogenesis, we also offer curated panels of assays to streamline your workflow.

For virus detection and quantitation, we currently offer three predesigned gene expression assays for SARS-CoV-2 viral gene targets.

Viral gene targetAssay ID
SARS-CoV-2N (N gene)vi07918637_s1
SARS-CoV-2S (S gene)vi07918636_s1
Orf1ab geneAPH6D4Y

The first two assays listed are also available as part of the following inventoried panels:

PanelDescription
TrueMark Respiratory Panel 2.0, OpenArray plateCharacterization of 32 respiratory tract viral and bacterial microbes
TrueMark Respiratory Panel 2.0, TaqMan Array cardCharacterization of 41 respiratory tract viral, bacterial, and fungal microbes

To study differential gene expression of host targets, our predesigned TaqMan Gene Expression assay portfolio includes over 2.3 million pre-designed primer/probe sets covering more than 30 species.  

A selection of some the most-cited genes related to SARS-CoV-2 research are listed in the table below. Many of these genes are also available in our curated panels for simultaneous analysis of multiple host genes implicated in SARS-CoV-2 infection.

Viral entry factorsRestriction factorsCytokinesPro-inflammatory & cytotoxic mediatorsChemokines & receptorsAdditional targets
ACE2 (232)BST2 (36)IL1B (77)GNLY (21)CCL2 (20)HGF  (217)
ANPEP (220)CH25H (18)IL2 (51)GZMA (51)CCL3 (12)IFIT1 (13)
BSG (85)CLEC4D (44)IL4 (55)GZMB (18)CCL5 (36)IFNGR1 (91)
CLEC4G (78)DNAJC6 (220)IL5 (46)GZMK (43)CCL11 (23)IFNGR2 (61)
CTSB (118)ELF1 (118)IL6 (58)CXCL3 (11)CCL20 (44)IFT43 (133)
CTSL (50)IFIT3 (15)IL7 (66)CXCL9 (38)CCL27 (29)ISG15 (15)
DPP4 (340)IFITM1 (11)IL8 (53) /
CXCL8 (40)
IFNB1 (16)CCR1 (21)KRT4 (63)
FURIN (173)IFITM2 (5)IL10 (66)IFNG (48)CCR5 (22)KRT7 (57)
NRP1 (227)IFITM3 (11)IL12 (186)KLRB1 (27)CXCL1 (17)SCGF (8)
TMPRSS11A (51)LY6E (28)IL13 (45)KLRC1 (31)CXCL3(11)STAT1 (292)
TMPRSS11B (47)REC8 (218)IL16 (164)KLRC2 (10)CXCL9 (38)VEGF (166
TMPRSS2 (124)ZBP1 (76)IL18 (39)KLRD1 (44)CXCL10 (41) 
TMPRSS4 (136)ZC3HAV1 (149) m-CSF (63)CXCL12 (48) 
   MIF (26)  
   PRF1 (21)  
   TGFB1 (83)  
   TGFB2 (86)  
   TNF (58)  
   TNFSF10 (63)  

Don’t see your gene of interest? Search for other predesigned assays by gene or assay ID ›

TaqMan flexible arrays include a curated and scientifically selected list of gene expression assays from the most-cited genes related to specific signaling pathways or disease states. Panels are available in multiple configurations and species, and are modifiable to easily add or delete assays/genes of interest, or to change your desired layout.

We currently offer three TaqMan® flexible content panels specific to coronavirus research:

Panel

Description

Genes

Host species

Coronavirus Entry Factor

13 of the most-cited host factors that SARS-CoV-2 and other coronaviruses hijack to infect a cell

ACE2, TMPRSS2, TMPRSS4, TMPRSS11A, TMPRSS11B, BSG, ANPEP, CLEC4G, FURIN, CTSL, CTSB, DPP4, and NRP1

Human
Mouse
Rat

Coronavirus Restriction Factors

13 of the most-cited antiviral host factors that are known to inhibit various stages of the coronavirus life cycle

LY6E, IFITM1, IFITM2, IFITM3, ZAP / ZC3HAV1, BST2, CLEC4D, ELF1, REC8, IFIT3, DNAJC6, ZBP1, CH25HHuman
Mouse
Rat

Coronavirus Immune Signaling

29 cytokines, chemokines, and growth factors involved in the immune response to SARS-CoV-2 and other coronaviruses

IL1B, IL2, IL4, IL5, IL6, IL7, IL10, IL12, IL13, IL16, IL18, IFNB1, IFNg, TNF, TGFB1, M-CSF/CSF1R, MIF, VEGF, SCGF, HGF, TRAIL/TNFSF10, CCL2, CCL3 / MIP1a, CCL5, CCL11, CCL27, CXCL1, CXCL10, CXCL12

Human
Mouse
Rat

In addition to Coronavirus flexible content panels, we offer various inventoried TaqMan panels in both card and plate formats for gene expression analysis of immune signaling pathways.
Learn more ›

You can also browse our comprehensive database for other applicable flexible panels.
Learn more ›

If you are unble to find a predesigned TaqMan Assay for your target of interest, we have two options that enable customization while retaining the quality, reproducibility, and gold-standard chemistry you have come to expect from TaqMan reagents.

  • Custom TaqMan Gene Expression Assays: Use our Custom TaqMan Assay Design Tool to leverage the exact design pipeline of our predesigned real-time PCR 5' nuclease TaqMan assays. Provide us with your target sequence of interest, then submit for assay design.
    Learn more ›

  • Custom primers and probes: Use your own design pipeline, then choose from our collection of dual-labeled TaqMan probes and unlabeled oligos for use as real-time PCR primers.
    Learn more ›

For gene expression analysis, we recommend the following assays as positive controls to monitor RNA purification efficacy and ensure the absence of real-time PCR inhibitors  

Positive controlAssay ID
Xeno ControlAc00010014_a1
Human RNase P ControlHs04930436_g1

Select a master mix

The master mix used for gene expression analysis depends on whether you want to perform 1-step real-time RT-PCR or 2-step real-time RT-PCR. A 1-step workflow reduces contamination and speeds up overall RT-PCR run time, whereas a 2-step workflow allows you to save your cDNA. If you perform 2-step real-time RT-PCR, you will also need to buy an additional master mix for the reverse-transcription reaction.

Learn more about 1-step and 2-step real-time RT-PCR ›
Learn more about reverse transcription products for 2-step real-time PCR ›

We recommend the following master mixes for most gene expression analysis needs. But you should also review the documentation provided with your assay for any specific workflow requirements.

Explore solutions for every step of the workflow:

Try our best performing TaqMan Fast Advanced Master Mix. Request a sample ›

Request a sample for translational research ›

*General purpose reagents manufactured in an ISO13485 facility and are labelled for laboratory use.

Real-time PCR and data analysis

We offer real-time PCR instruments for all research needs, from simplicity on a budget to high throughput with maximum productivity.
Learn more ›

Once you order your assays, we provide the protocols and documentation specific to your assay format for download.
Learn more ›

For data analysis, we recommend the Quantstudio Design & Analysis (DA2) app on Connect, our cloud-based platform.

COL111051-QS-Pro-FHRamily-4-v2-F-650x600

Gene expression analysis requires high-quality RNA for real-time RT-PCR. Select the RNA isolation method that is best suited to your sample type and throughput needs.

Learn more ›

TaqMan Gene Expression Assay selection

Our Applied Biosystem TaqMan Gene Expression Assays consist of target primers and an optimized sequence-specific probe (with no extra design, optimization, or melt-curve analysis needed). Explore predesigned assays for the curated list of genes associated with SARS-CoV-2 viral and host target research below, or search our database of more than 2.3 million gene expression assays for additional targets of interest. TaqMan Assays are available in four format options  to meet your experiment through-put needs: single-tube, 96-well plates (0.1 and 0.2 mL), TaqMan Array Cards or OpenArray plates. For simultaneous interrogation of multiple genes related to in SARS-CoV-2 infection and pathogenesis, we also offer curated panels of assays to streamline your workflow.

For virus detection and quantitation, we currently offer three predesigned gene expression assays for SARS-CoV-2 viral gene targets.

Viral gene targetAssay ID
SARS-CoV-2N (N gene)vi07918637_s1
SARS-CoV-2S (S gene)vi07918636_s1
Orf1ab geneAPH6D4Y

The first two assays listed are also available as part of the following inventoried panels:

PanelDescription
TrueMark Respiratory Panel 2.0, OpenArray plateCharacterization of 32 respiratory tract viral and bacterial microbes
TrueMark Respiratory Panel 2.0, TaqMan Array cardCharacterization of 41 respiratory tract viral, bacterial, and fungal microbes

To study differential gene expression of host targets, our predesigned TaqMan Gene Expression assay portfolio includes over 2.3 million pre-designed primer/probe sets covering more than 30 species.  

A selection of some the most-cited genes related to SARS-CoV-2 research are listed in the table below. Many of these genes are also available in our curated panels for simultaneous analysis of multiple host genes implicated in SARS-CoV-2 infection.

Viral entry factorsRestriction factorsCytokinesPro-inflammatory & cytotoxic mediatorsChemokines & receptorsAdditional targets
ACE2 (232)BST2 (36)IL1B (77)GNLY (21)CCL2 (20)HGF  (217)
ANPEP (220)CH25H (18)IL2 (51)GZMA (51)CCL3 (12)IFIT1 (13)
BSG (85)CLEC4D (44)IL4 (55)GZMB (18)CCL5 (36)IFNGR1 (91)
CLEC4G (78)DNAJC6 (220)IL5 (46)GZMK (43)CCL11 (23)IFNGR2 (61)
CTSB (118)ELF1 (118)IL6 (58)CXCL3 (11)CCL20 (44)IFT43 (133)
CTSL (50)IFIT3 (15)IL7 (66)CXCL9 (38)CCL27 (29)ISG15 (15)
DPP4 (340)IFITM1 (11)IL8 (53) /
CXCL8 (40)
IFNB1 (16)CCR1 (21)KRT4 (63)
FURIN (173)IFITM2 (5)IL10 (66)IFNG (48)CCR5 (22)KRT7 (57)
NRP1 (227)IFITM3 (11)IL12 (186)KLRB1 (27)CXCL1 (17)SCGF (8)
TMPRSS11A (51)LY6E (28)IL13 (45)KLRC1 (31)CXCL3(11)STAT1 (292)
TMPRSS11B (47)REC8 (218)IL16 (164)KLRC2 (10)CXCL9 (38)VEGF (166
TMPRSS2 (124)ZBP1 (76)IL18 (39)KLRD1 (44)CXCL10 (41) 
TMPRSS4 (136)ZC3HAV1 (149) m-CSF (63)CXCL12 (48) 
   MIF (26)  
   PRF1 (21)  
   TGFB1 (83)  
   TGFB2 (86)  
   TNF (58)  
   TNFSF10 (63)  

Don’t see your gene of interest? Search for other predesigned assays by gene or assay ID ›

TaqMan flexible arrays include a curated and scientifically selected list of gene expression assays from the most-cited genes related to specific signaling pathways or disease states. Panels are available in multiple configurations and species, and are modifiable to easily add or delete assays/genes of interest, or to change your desired layout.

We currently offer three TaqMan® flexible content panels specific to coronavirus research:

Panel

Description

Genes

Host species

Coronavirus Entry Factor

13 of the most-cited host factors that SARS-CoV-2 and other coronaviruses hijack to infect a cell

ACE2, TMPRSS2, TMPRSS4, TMPRSS11A, TMPRSS11B, BSG, ANPEP, CLEC4G, FURIN, CTSL, CTSB, DPP4, and NRP1

Human
Mouse
Rat

Coronavirus Restriction Factors

13 of the most-cited antiviral host factors that are known to inhibit various stages of the coronavirus life cycle

LY6E, IFITM1, IFITM2, IFITM3, ZAP / ZC3HAV1, BST2, CLEC4D, ELF1, REC8, IFIT3, DNAJC6, ZBP1, CH25HHuman
Mouse
Rat

Coronavirus Immune Signaling

29 cytokines, chemokines, and growth factors involved in the immune response to SARS-CoV-2 and other coronaviruses

IL1B, IL2, IL4, IL5, IL6, IL7, IL10, IL12, IL13, IL16, IL18, IFNB1, IFNg, TNF, TGFB1, M-CSF/CSF1R, MIF, VEGF, SCGF, HGF, TRAIL/TNFSF10, CCL2, CCL3 / MIP1a, CCL5, CCL11, CCL27, CXCL1, CXCL10, CXCL12

Human
Mouse
Rat

In addition to Coronavirus flexible content panels, we offer various inventoried TaqMan panels in both card and plate formats for gene expression analysis of immune signaling pathways.
Learn more ›

You can also browse our comprehensive database for other applicable flexible panels.
Learn more ›

If you are unble to find a predesigned TaqMan Assay for your target of interest, we have two options that enable customization while retaining the quality, reproducibility, and gold-standard chemistry you have come to expect from TaqMan reagents.

  • Custom TaqMan Gene Expression Assays: Use our Custom TaqMan Assay Design Tool to leverage the exact design pipeline of our predesigned real-time PCR 5' nuclease TaqMan assays. Provide us with your target sequence of interest, then submit for assay design.
    Learn more ›

  • Custom primers and probes: Use your own design pipeline, then choose from our collection of dual-labeled TaqMan probes and unlabeled oligos for use as real-time PCR primers.
    Learn more ›

For gene expression analysis, we recommend the following assays as positive controls to monitor RNA purification efficacy and ensure the absence of real-time PCR inhibitors  

Positive controlAssay ID
Xeno ControlAc00010014_a1
Human RNase P ControlHs04930436_g1

Select a master mix

The master mix used for gene expression analysis depends on whether you want to perform 1-step real-time RT-PCR or 2-step real-time RT-PCR. A 1-step workflow reduces contamination and speeds up overall RT-PCR run time, whereas a 2-step workflow allows you to save your cDNA. If you perform 2-step real-time RT-PCR, you will also need to buy an additional master mix for the reverse-transcription reaction.

Learn more about 1-step and 2-step real-time RT-PCR ›
Learn more about reverse transcription products for 2-step real-time PCR ›

We recommend the following master mixes for most gene expression analysis needs. But you should also review the documentation provided with your assay for any specific workflow requirements.

Explore solutions for every step of the workflow:

Try our best performing TaqMan Fast Advanced Master Mix. Request a sample ›

Request a sample for translational research ›

*General purpose reagents manufactured in an ISO13485 facility and are labelled for laboratory use.

Real-time PCR and data analysis

We offer real-time PCR instruments for all research needs, from simplicity on a budget to high throughput with maximum productivity.
Learn more ›

Once you order your assays, we provide the protocols and documentation specific to your assay format for download.
Learn more ›

For data analysis, we recommend the Quantstudio Design & Analysis (DA2) app on Connect, our cloud-based platform.

COL111051-QS-Pro-FHRamily-4-v2-F-650x600