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500 ng total RNA was amplified using the MessageAmp modified Eberwine linear amplification procedure (Applied Biosystems).
The ds cDNA is then amplified using a linear amplification procedure.
Hybridization was performed overnight according to the Agilent, Low NA input Linear Amplification procedure at 65°C.
We developed a method to prepare and label miRNA targets using a linear amplification procedure in which an antisense-labelled target is produced.
The resulting RNA samples were amplified using a conventional in vitro transcription-mediated linear amplification procedure (MessageAmp II, Life Technologies), reciprocally labeled with AlexaFluor 546 or AlexaFluor 647 (Life Technologies) for induced allergy and control samples and hybridized to mouse whole-genome gene expression arrays (SurePrint G3Mouse GE 8x60K Kit, Agilent).
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However, these methods employ either lengthy linear amplification procedures, or primer extension (4 cycles) and 15 cycles of PCR – all prior to a standard Illumina library prep entailing a further 17 18 cycles of PCR.
The established Affymetrix linear amplification procedures using the GeneChip® Expression 3'-Amplification Two-Cycle cDNA Synthesis kit yielded closely similar profiles between the five replicates of the same treatment (Pearson's correlation coefficients of the range 0.914 to 0.949), indicating a highly reproducible procedure.
Rare sequences are enriched by slower hybridization and the non-hybridized RNA is recovered and amplified by a linear RNA amplification procedure, which minimizes the biased exponential amplification of subsets of genes in a mixture.
Labelled miRNAs were prepared either by a procedure involving linear amplification of miRNAs (labelled-aRNA) or using a direct labelling strategy (labelled-cDNA) and analysed using a custom miRNA microarray platform.
The sequence specificity of UV-induced DNA damage was investigated in a specifically designed DNA plasmid using two procedures: end-labelling and linear amplification.
Following the reproducible procedures of RNA extraction and linear amplification from our previous study [ 43], we isolated total RNA from individual oocytes/embryos using TRIzol (Invitrogen, Grand Island, NY) and co-precipitated the RNA with linear acrylamide (Ambion).
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