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Microarray hybridization was performed using the Affymetrix GeneChip Yeast Genome S98 Array using protocols described by Affymetrix (Santa Clara, CA).
Amplification and sequencing of nuclear 18S and 28S genes was carried out using protocols described by Struck et al. [ 24].
A set of physiological characteristics including catalase and oxidase tests and nitrate reduction were assessed using protocols described by Shieh et al. [ 17].
Three-week-old Balb/C female mice were anesthetized, and their inguinal mammary glands were cleared of host epithelium by using protocols described by Smith et al. [ 18- 20] (three mice per condition; six cleared mammary fat pads).
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DNA fragmentation was evaluated by using protocol described by McGahon et al. (1995) with modification.
Total RNA for both NimbleGen microarray hybridization and real-time qPCR experiments was isolated using protocol described by Chang et al. [ 47].
Insect attack was done using protocol described by Babin et al. [ 55]. - P7, IMC47, UPA134 are Forastero genotypes originated from the Upper Amazonian region of Peru, known for their resistance to Phytophthora palmivora or P. megakarya.
The cDNA was synthesized using protocol described by a Thermo Scientific RevertAid Reverse Transcriptase kit (Thermo Fisher Scientific, Waltham, MA, USA). 1 μl of diluted cDNA (1 5) was used in each real time-PCR, using a THUNDERBIRD SYBR qPCR Mix (Toyobo, Life Science, Osaka, Japan), and an Illumina Eco Real-Time PCR Instrument (Illumina, San Diego, CA, USA).
The cotton dust samples were assayed using the kinetic limulus amoebocyte lysate assay using standard protocols described by Thorne (2000).
The expression of genes from individual brains was assessed using the double-spotted Apis mellifera brain 9K version 3.0 cDNA microarray using the protocols described by Whitfield et al. [ 11], Grozinger et al. [ 18] and Cash et al. [ 12].
Different physiochemical parameters were evaluated using standard protocols described by the American Public Health Association (APHA) (Eaton 2005).
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