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Adult worms were homogenized in 1 mL Trizol (Invitrogen), and RNA was isolated using organic extraction followed by column purification using an RNeasy Mini Kit (Qiagen) including the on-column DNase digest.
In short, RNA was extracted by column purification using the RNeasy micro kit (Qiagen, Hilden, Germany) and RNA transcribed into cDNA.
For the POP369 population, DNA from 94 full-sibs and the pollen parent was purified from young leaves using a CTAB (hexadecyltrimethylammonium bromide) extraction method [ 54], followed by column purification using the NucleoSpin® kit (Macherey-Nagel GmbH & Co. KG).
Briefly, worms were homogenized by bead-beating in TRIzol (Invitrogen, Carlsbad, CA) and RNA was isolated by organic extraction with 1-bromo-3-chloropropane followed by column purification using the RNeasy Mini Kit (Qiagen) including an on-column DNase digest.
The NEBNext DNA Sample Prep Reagent Set 1 was used with incubation times for end repair and A-tail stages of one hour and a two hour ligation step, each step was followed by column purification using QIAquick spin columns (QIAGEN).
Total RNA was extracted from the sorted cell populations with Trizol reagent (Invitrogen, Burlington, Canada) followed by column purification using the Qiagen RNeasy Kit (QIAGEN, Mississauga, Canada) and processed for hybridization to Affymetrix GeneChip® Mouse Genome 430 2.0 arrays (Genome Quebec Innovation Centre, Montreal, Canada).
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PCR products from the variable 18S rRNA and COWP gene loci were cleaned by spin column purification using the QIAquick PCR Purification kits (Qiagen).
Additional total RNA was harvested using Trizol Life Technologiess) according to the manufacturer's instruction, DNase treated (Roche, Welwyn Garden City, UK) followed by on column purification using RNeasy RNA extraction kit (Qiagen, Manchester, UK).
The reaction was stopped after 5 min at room temperature by the addition of 50 μl 50 mM ethylenediaminetetraacetate acid (EDTA), followed by PD-10 column purification using 0.25 M NaOAc with 5 mg ml−1 gentisic acid, pH 5.5, as eluant.
RNA purification was performed by extraction with TriReagent (Sigma, St . Louis MO) followed by chloroform extraction and column purification using the RNeasy Kit (Qiagen, Germantown, MD) (Plank et al., 2013).
Plasma RNA was extracted using TRIzol LS followed by column purification.
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