The largest database of trusted experimental protocols

6 protocols using quantstudio 3d analysis suite

1

Digital RT-PCR for GSDMB Isoform Quantification

Check if the same lab product or an alternative is used in the 5 most similar protocols
To measure GSDMB Δ5–8 isoform levels and total GSDMB transcript, digital RT-PCR reactions were performed on a QuantStudio 3D Digital PCR System (Thermo Fisher Scientific) using the QuantStudio 3D Digital PCR Master Mix (Thermo Fisher Scientific) and 1 μL of cDNA as template. Custom TaqMan assays were designed to amplify GSDMB Δ5–8 isoform and total GSDMB isoforms. The sequences of primers and probes used in digital RT-PCR assays are listed in Supplementary Table S1.
Each reaction mixture was loaded onto a QuantStudio 3D Digital PCR Chip (Thermo Fisher Scientific) and cycled for 40 cycles using standard conditions. End-point fluorescence data were analyzed through the QuantStudio 3D Digital PCR Instrument and the QuantStudio 3D Analysis Suite (Thermo Fisher Scientific), according to the manufacturer’s instructions.
+ Open protocol
+ Expand
2

Digital PCR for mtDNA quantification

Check if the same lab product or an alternative is used in the 5 most similar protocols
The detailed method was described previously49 (link). All primers and probes were ordered
from IDT (Coralville, Iowa). The 3D digital PCR was used according to the
manufacturer’s protocol. QuantStudio 3D Digital
PCR Master Mix v2 and individual QuantStudio 3D digital PCR 20K Chip kit v2
were purchased from Thermo scientific (Applied Biosystems, Waltham, MA).
Prepared sample mix was loaded into ChIP using QuantStudio 3D Digital PCR
Chip Loader (Thermo scientific). Chip PCR amplification was performed in a
ProFlex PCR System (96 °C for 10 min; 39 cycles of 60 °C for 2
min and 98 °C for 30 sec; and 60 °C for 2 min). After
amplification, each chip was loaded into the QuantStudio 3D Digital reader.
Data were analyzed using QuantStudio 3D Analysis Suite (Thermo scientific).
All biological repeats were performed in at least triplicate.

ΔmtDNA primers F: TTGCTTTTTCTTTATATGTTTTG; R:
TTTATTTAATTTGGTTAAACAAGAGGT. ΔmtDNA probes 5’
6-FAM/ZEN/3’ IBFQ:
/56-FAM/AGGATCGTA/ZEN/ACATTTTATTTTTTTGCTTTA/3IABkFQ/.

Wildtype primers F: GCTTTTTCTTTATATGTTTTGTG.

R: TCACCTTCAGAAAAATCAAATGG wildtype mtDNA probes
5’ HEX/ZEN/3’ IBFQ:
/5HEX/AATTATAGT/ZEN/AATTGCTGAACTTAACCGGGC/3IABkFQ/

+ Open protocol
+ Expand
3

Quantitative RT-PCR Analysis of Cardiac Biomarkers

Check if the same lab product or an alternative is used in the 5 most similar protocols
Reverse transcription-quantitative (RT-q)PCR was performed to detect mRNA levels of miR-155, atrial natriuretic peptide (ANP), B-type natriuretic peptide (BNP) and B-myosin heavy chain (B-MHC). Primer3 Plus (http://www.primer3plus.com/cgi-bin/dev/primer3plus.cgi) was used to design the primers. According to the manufacturer's protocol, mouse myocardial tissues or isolated rat ventricular myocytes (NRVMs, 1×106) were treated with TRIzol® (cat. no. 15596026; Thermo Fisher Scientific, Inc.) to extract total RNA. According to the manufacturer's protocol, reverse transcription of RNA was then performed using a miRNA reverse transcription kit (cat. no. 4366597; Thermo Fisher Scientific, Inc.) and PrimeScript RT-PCR kit (cat. no. RR014A; Takara Bio, Inc.). The cDNA was used as a template and RT-qPCR was performed on QuantStudio 3D PCR system (Thermo Fisher Scientific, Inc.) with QuantStudio 3D AnalysisSuite (Thermo Fisher Scientific, Inc.). qPCR thermocycling conditions were as follows: Denaturation at 94°C for 5 min, 37 cycles of 95°C for 15 sec, 60°C for 30 sec and 72°C for 30 sec. All reactions were repeated three times. U6 and GAPDH were the internal controls. The relative expressions of miR-155, ANP, BNP and B-MHC were expressed as a function of cycle quantification (Cq) and analyzed by the 2−ΔΔCq method (27 (link)). The primers are listed in Table I.
+ Open protocol
+ Expand
4

Digital PCR for mtDNA quantification

Check if the same lab product or an alternative is used in the 5 most similar protocols
The detailed method was described previously49 (link). All primers and probes were ordered
from IDT (Coralville, Iowa). The 3D digital PCR was used according to the
manufacturer’s protocol. QuantStudio 3D Digital
PCR Master Mix v2 and individual QuantStudio 3D digital PCR 20K Chip kit v2
were purchased from Thermo scientific (Applied Biosystems, Waltham, MA).
Prepared sample mix was loaded into ChIP using QuantStudio 3D Digital PCR
Chip Loader (Thermo scientific). Chip PCR amplification was performed in a
ProFlex PCR System (96 °C for 10 min; 39 cycles of 60 °C for 2
min and 98 °C for 30 sec; and 60 °C for 2 min). After
amplification, each chip was loaded into the QuantStudio 3D Digital reader.
Data were analyzed using QuantStudio 3D Analysis Suite (Thermo scientific).
All biological repeats were performed in at least triplicate.

ΔmtDNA primers F: TTGCTTTTTCTTTATATGTTTTG; R:
TTTATTTAATTTGGTTAAACAAGAGGT. ΔmtDNA probes 5’
6-FAM/ZEN/3’ IBFQ:
/56-FAM/AGGATCGTA/ZEN/ACATTTTATTTTTTTGCTTTA/3IABkFQ/.

Wildtype primers F: GCTTTTTCTTTATATGTTTTGTG.

R: TCACCTTCAGAAAAATCAAATGG wildtype mtDNA probes
5’ HEX/ZEN/3’ IBFQ:
/5HEX/AATTATAGT/ZEN/AATTGCTGAACTTAACCGGGC/3IABkFQ/

+ Open protocol
+ Expand
5

Real-Time and Digital PCR for Gene Expression

Check if the same lab product or an alternative is used in the 5 most similar protocols
Extraction of RNA was performed from VECs and VICs using the Total RNA Purification Plus Kit (Norgen Biotek Corp.). RNA was quantified using Nanodrop and used for two steps PCR amplification with TaqMan Reverse Transcription Reagent kit (Life Technologies). Total RNA (1 μg) was converted into cDNA. Real Time PCR (qPCR) was performed on ABI Prism 7900 HT (Applied Biosystems), according to the manufacturer’s instructions and analysis were performed using software SDS2.4 (Life Technologies). Digital PCR (dPCR) was performed on a QuantStudio™ 3D Digital PCR System platform composed by the QuantStudio™ 3D Instrument, the Dual Flat Block GeneAmp® PCR System 9700 and the QuantStudio™ 3D Digital PCR Chip Loader (Life Technologies). dPCR was performed according to the manufactures’s instructions and analysis were executed with QuantStudio® 3D AnalysisSuite™ (Life Technologies). Primers labelled with FAM® dyes were used to evaluate the expression of target genes, while for housekeeping genes primers labelled with VIC® dye were implemented. For normalization we used glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and ribosomal protein large P0 (RPLP0) gene expression levels and the primers used are listed in Supplemental Table 3
+ Open protocol
+ Expand
6

SARS-CoV-2 sgRNA Detection by Digital PCR

Check if the same lab product or an alternative is used in the 5 most similar protocols
The presence of sg-RNA was assessed by specific retrotranscription (see [12 (link)]) and digital PCR (dPCR) in 122 longitudinal RNA samples from a sub-cohort of 36 individuals characterized by age, sex distribution and basal viral load compared to those of the whole cohort. The resulting cDNAs were then tested by means of chip-based dPCR using TaqMan assays specific for N and E genes on QuantStudio 3D Digital PCR System (Life Technologies, Carlsbad, CA, USA). In particular, 6 µL of each cDNA was combined with QuantStudio™ 3D Digital PCR Master Mix (Life Technologies) and the TaqMan assay specific for N or E gene and, then, loaded on QuantStudio™ 3D Digital PCR Chips according to manufacturer’s instructions. Each sample was tested in duplicate on two different chips. Loaded samples were then amplified on ProFlex PCR system (Life Technologies) and the end-point fluorescent data were analyzed by QuantStudio™ 3D Digital PCR Instrument (Life Technologies) and the QuantStudio™ 3D AnalysisSuite™ (Life Technologies).
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!