Journal: Methods (San Diego, Calif.)

Article Title: In pursuit of sensitivity: Lessons learned from viral nucleic acid detection and quantification on the Raindance ddPCR platform

doi: 10.1016/j.ymeth.2021.04.008

Figure Lengend Snippet: DNA input upper limit test on the Raindance ddPCR platform. Each 50 μL, SIV and CCR5 duplex ddPCR reaction was loaded with 1 million to 8 million cell equivalent genomic DNA extracted from the duodenum of an SIVmac239-infected rhesus macaque (animal 313–08) that was treated with combination antiretrovirals. Note that as the input DNA amount was progressively increased, the separation between clusters was less distinct, and when the total DNA input in each reaction was 5 million cell equivalent or more, there were no distinct signal clusters. SIV+, target cluster containing SIV signal. SIV+ CCR5+, dual occupancy cluster.

Article Snippet: In sections 2, 3 and 4, technical considerations for achieving maximal detection sensitivity are detailed in part based on the Raindance ddPCR platform.

Techniques: Infection

Journal: Methods (San Diego, Calif.)

Article Title: In pursuit of sensitivity: Lessons learned from viral nucleic acid detection and quantification on the Raindance ddPCR platform

doi: 10.1016/j.ymeth.2021.04.008

Figure Lengend Snippet: The effect of high occupancy setting on cluster separation. The high occupancy (HO) setting during the “sense” step was used to alleviate the “cluster-squeeze” issue caused by large template DNA input in Raindance ddPCR reactions (A-D, no HO setting; E-H, HO setting). Note that in the 1 million cell to 3 million cell equivalent DNA input range tested, the HO setting did not lead to appreciably improved cluster separation.

Article Snippet: In sections 2, 3 and 4, technical considerations for achieving maximal detection sensitivity are detailed in part based on the Raindance ddPCR platform.

Techniques:

Journal: bioRxiv

Article Title: Detection of resistance in Phytophthora infestans to the carboxylic acid amide (CAA) fungicides using digital droplet PCR

doi: 10.1101/2025.01.13.630889

Figure Lengend Snippet: Overview of the ddPCR workflow to detect for CAA resistance in Phytophthora infestans . A) DNA is prepared directly from pure P. infestans cultures, or infected leaf tissue or infected leaf tissue stamped onto FTA cards following an initial nested PCR, B) DNA is loaded into a Stilla system and undergo sample partition and PCR, C) a combination of three dual-labelled probes are used to detect for changes that can confer CAA resistance, with G1105S specifically targeted, D) the presence of droplets positive for the Pinfestans- Gen probe, in combination positive/negative droplets for either PiCesA3-WT or PiCesA3-G1105S determines the sensitivity status of the specific droplet. In the 2D-fluorescence plots presented droplets are positive for both Pinfestans- Gen (Red) and PiCesA3-G1105S (Green) and negative for PiCesA3-G1105S (Blue), confirming the sample contains G1105S and is resistant to the CAA fungicides.

Article Snippet: To exploit the potential of the Stilla nacia 3-colour ddPCR Platform (Stilla Technologies, Villejuif, France) a multiplex PCR was designed with three probes, P. infestans -Gen labelled with Cy5 to allow the detection of PiCesA3 irrespective of CAA sensitivity status, PiCesA3-WT labelled with FAM to detect CesA3-WT and PiCesA3-G1105S labelled with HEX to detect CesA3-mutant (see ), thus allowing for detection of additional potential alterations at position 1105 that may confer CAA resistance.

Techniques: Infection, Nested PCR, Fluorescence

Journal: Methods (San Diego, Calif.)

Article Title: In pursuit of sensitivity: Lessons learned from viral nucleic acid detection and quantification on the Raindance ddPCR platform

doi: 10.1016/j.ymeth.2021.04.008

Figure Lengend Snippet: DNA input upper limit test on the Raindance ddPCR platform. Each 50 μL, SIV and CCR5 duplex ddPCR reaction was loaded with 1 million to 8 million cell equivalent genomic DNA extracted from the duodenum of an SIVmac239-infected rhesus macaque (animal 313–08) that was treated with combination antiretrovirals. Note that as the input DNA amount was progressively increased, the separation between clusters was less distinct, and when the total DNA input in each reaction was 5 million cell equivalent or more, there were no distinct signal clusters. SIV+, target cluster containing SIV signal. SIV+ CCR5+, dual occupancy cluster.

Article Snippet: Due to the capacity to accommodate a large quantity of nucleic acid input and the ability to overcome inhibition, the RainDance platform-enabled ddPCR assays are well-positioned to detect low (e.g. single digit) level cell- and tissue-derived viral nucleic acids.

Techniques: Infection

Journal: Methods (San Diego, Calif.)

Article Title: In pursuit of sensitivity: Lessons learned from viral nucleic acid detection and quantification on the Raindance ddPCR platform

doi: 10.1016/j.ymeth.2021.04.008

Figure Lengend Snippet: The effect of high occupancy setting on cluster separation. The high occupancy (HO) setting during the “sense” step was used to alleviate the “cluster-squeeze” issue caused by large template DNA input in Raindance ddPCR reactions (A-D, no HO setting; E-H, HO setting). Note that in the 1 million cell to 3 million cell equivalent DNA input range tested, the HO setting did not lead to appreciably improved cluster separation.

Article Snippet: Due to the capacity to accommodate a large quantity of nucleic acid input and the ability to overcome inhibition, the RainDance platform-enabled ddPCR assays are well-positioned to detect low (e.g. single digit) level cell- and tissue-derived viral nucleic acids.

Techniques: