Amplification:Article Title: Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome.
Article Snippet: DNA concentration was measured using a Qubit dsDNA HS kit (Life Technologies Inc., Gaithersburg, MD, USA). .. A master mix for amplification was prepared using the Roche High Fidelity Fast Start Kit and 20X Access Array loading reagent according to Fluidigm protocols. .. Amplicon preparation of the V4 region of the prokaryotic 16S rRNA and fungal ITS rRNA genes was carried out using a Fluidigm Access Array IFC chip (Fluidigm) with single-index barcoded primers 515F (5′-GTG YCA GCMGCC GCG GTAA-3′) and 806R (5′-GGA CTA CNVGGG TWT CTAAT-3) [26], and primers ITS3-F′(5′-GCA TCG ATG AAG AAC GCA GC-3′) and ITS4-R′(5′-TCC TCC GCT TAT TGA TAT GC-3′) [27], respectively.
Article Title: Methods and systems for monitoring a recipient of an allograft
Article Snippet: .. Materials to be used for this amplification protocol include a Fluidigm Access Array, or chip, a high-fidelity polymerase such as FastStart High Fidelity (Roche), Expand High Fidelity (Roche), Phusion Flash II (ThermoFisher Scientific), Phusion Hot Start II (ThermoFisher Scientific), KAPA HiFi (Kapa BioSystems), or KAPA2G (Kapa Biosystems), 1× Access Array Harvest Solution (Fluidigm, PN 100-1031), 20× Access Array Loading reagent (Fluidigm), and the 226 primer pairs designed as described above. ..
Article Title: Methods and systems for monitoring a recipient of an allograft
Article Snippet: .. Materials used for this amplification protocol included a Fluidigm Access Array, or chip, the high-fidelity DNA polymerase FastStart High Fidelity (Roche), 1× Access Array Harvest Solution (Fluidigm, PN 100-1031), 20× Access Array Loading reagent (Fluidigm), and the 266 primer pairs designed as described above. ..
Article Title: Methods and systems for monitoring a recipient of an allograft
Article Snippet: DNA Amplification The cell-free DNA from the pre-amplification was amplified according to the Fluidigm Access Array process and protocols (See page 63 of Access Array System for Illumina Sequencing System). .. Materials used for this amplification protocol included a Fluidigm Access Array, or chip, the high-fidelity DNA polymerase Phusion Flash II (ThermoFisher Scientific), 1× Access Array Harvest Solution (Fluidigm, PN 100-1031), 20× Access Array Loading reagent (Fluidigm), and the 266 primer pairs designed as described above. .. Instruments used for this amplification protocol included two IFC Controller AX (Fluidigm) and one FC1 cycler (Fluidigm).
Article Title: Altering plant carbon allocation to stems has distinct effects on rhizosphere soil microbiome assembly, interactions, and potential functions in sorghum
Article Snippet: DNA concentration was measured using a Qubit dsDNA HS kit (Life Technologies Inc., Gaithersburg, MD, USA). .. A master mix for amplification was prepared using the Roche High Fidelity Fast Start Kit and 20X Access Array loading reagent according to Fluidigm protocols. .. Amplicon preparation of the V4 region of the prokaryotic 16S rRNA and fungal ITS rRNA genes was carried out using a Fluidigm Access Array IFC chip (Fluidigm) with single- index barcoded primers 515F (5′- GTGYCAGCMGCCGCGGTAA- 3′) (Parada et al., 2016) and 806R (5′- GGACTACNVG GGTWTCTAAT- 3′) (Apprill et al., 2015; Vilgalys, 1994) and primers ITS3 (5′- GCATCGATGAAGAACGCAGC- 3′) and ITS4 (5′- TCCTCCGCTTATTGATATGC- 3′) (Gardes & Bruns, 1993), respectively.
Article Title: Methods and systems for monitoring a recipient of an allograft
Article Snippet: DNA Amplification The cell-free DNA is amplified according to the Fluidigm Access Array process and protocols (See page 63 of Access Array System for Illumina Sequencing System). .. Materials to be used for this amplification protocol include a Fluidigm Access Array, or chip, FastStart High Fidelity PCR system (Roche), 1× Access Array Harvest Solution (Fluidigm, PN 100-1031), 20× Access Array Loading reagent (Fluidigm), and the 92 primer pairs designed as described above. .. Instruments to be used for this amplification protocol include two IFC Controller AX (Fluidigm) and one FC1 cycler (Fluidigm).
Polymerase Chain Reaction:Article Title: Nucleic acid encoding reactions
Article Snippet: Preparing Amplicons The following documents may be consulted as references for this protocol: Fluidigm® IFC Controller for ACCESS ARRAYTM System User Guide (PN 68000157); Fluidigm® Control Line Fluid Loading Procedure Quick Reference (PN68000132); and Agilent DNA 1000 Kit Guide. .. The following Reagents were used for this protocol and were stored at −20° C.: FastStart High Fidelity PCR System, dNTPack (Roche, PN 04-738-292-001); 20× ACCESS ARRAYTM Loading Reagent (Fluidigm, PN 100-0883); 1× ACCESS ARRAYTM Harvest Solution (Fluidigm, PN 100-1031); ACCESS ARRAYTM Barcode Library for Illumina Sequencers—384 (Bidirectional) (Fluidigm, PN 100-3771); target-specific primer pairs tagged with universal tags (CS1 forward tag, CS2 reverse tag), including 50 μM CS1-Tagged TS Forward Primer and 50 μM CS2-Tagged TS Reverse Primer; and template DNA at 50 ng/μL. (The 1× ACCESS ARRAYTM Harvest Solution (Fluidigm, PN 100-1031) is not packaged for individual sale. ..
Article Title: Nucleic acid encoding reactions
Article Snippet: .. Preparing and Sequencing Amplicons The following reagents were used for this protocol and were stored at −20° C.: FastStart High Fidelity PCR System, dNTPack (Roche, PN 04-738-292-001); 20× ACCESS ARRAYTM Loading Reagent (Fluidigm, PN 100-0883); Target-specific primer pairs with universal tags (CS1 forward tag, CS2 reverse tag), including 50 μM CS1-Tagged TS Forward Primer and 50 μM CS2-Tagged TS Reverse Primer; and Bidirectional 384 Barcode Kit for the Illumina GAIT, HiSeq and MiSeq Sequencers (Fluidigm, PN 100-3771). .. Additional reagents were stored at 4° C., including: Agilent DNA 1000 Kit Reagents (Agilent, PN 5067-1504); and 1× ACCESS ARRAYTM Harvest Solution (Fluidigm, PN 100-1031).
Article Title: Methods and systems for monitoring a recipient of an allograft
Article Snippet: DNA Amplification The cell-free DNA is amplified according to the Fluidigm Access Array process and protocols (See page 63 of Access Array System for Illumina Sequencing System). .. Materials to be used for this amplification protocol include a Fluidigm Access Array, or chip, FastStart High Fidelity PCR system (Roche), 1× Access Array Harvest Solution (Fluidigm, PN 100-1031), 20× Access Array Loading reagent (Fluidigm), and the 92 primer pairs designed as described above. .. Instruments to be used for this amplification protocol include two IFC Controller AX (Fluidigm) and one FC1 cycler (Fluidigm).
Sequencing:Article Title: Nucleic acid encoding reactions
Article Snippet: .. Preparing and Sequencing Amplicons The following reagents were used for this protocol and were stored at −20° C.: FastStart High Fidelity PCR System, dNTPack (Roche, PN 04-738-292-001); 20× ACCESS ARRAYTM Loading Reagent (Fluidigm, PN 100-0883); Target-specific primer pairs with universal tags (CS1 forward tag, CS2 reverse tag), including 50 μM CS1-Tagged TS Forward Primer and 50 μM CS2-Tagged TS Reverse Primer; and Bidirectional 384 Barcode Kit for the Illumina GAIT, HiSeq and MiSeq Sequencers (Fluidigm, PN 100-3771). .. Additional reagents were stored at 4° C., including: Agilent DNA 1000 Kit Reagents (Agilent, PN 5067-1504); and 1× ACCESS ARRAYTM Harvest Solution (Fluidigm, PN 100-1031).
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