DNA was extracted from the lignin, xylan, and unamended enrichments. Replicates were pooled together to get enough DNA for sequencing. After the incubation, 50 ml of each consortia was harvested into pellets by high speed centrifugation at 8000 rpm. DNA was extracted from each of the pellets using a ZR-DuetTM DNA/RNA MiniPrep Kit (Zymo Research Corp., Irvine, CA, United States) following the manufacturer’s instructions. DNA was cleaned of any contaminants using a OneStepTM PCR Inhibitor Kit (Zymo Research Corp., Irvine, CA, United States) and then concentrated using a Genomic DNA Clean and Concentrate Kit (Zymo Research Corp., Irvine, CA, United States). DNA was prepared into two aliquots, one for 16s rRNA gene amplicon sequencing and the other for metagenomics.
Genomic dna clean and concentrate kit
Manufactured by Zymo Research
Sourced in United States
The Genomic DNA Clean and Concentrate Kit is a laboratory product designed to purify and concentrate genomic DNA from various sample types. It utilizes a silica-based membrane technology to selectively bind DNA, allowing for the removal of contaminants and the recovery of purified DNA.
Automatically generated - may contain errors
4 protocols using genomic dna clean and concentrate kit
1
DNA Extraction and Purification from Enrichments
2
Genomic DNA Preparation for WGS
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Isolates confirmed as C. jejuni were utilized for WGS. Each sample was RNase-treated by incubating 44 μl genomic DNA with 5 μl buffer and 1 μl RNase (Invitrogen – AM2294) for 1 h at 37°C before heat inactivating at 70°C for 20 min. The resulting RNase-treated DNA was cleaned using a Zymo Genomic DNA Clean and Concentrate Kit (D4011) following the manufacturer’s instructions. Genomic DNA sample concentrations were quantified on a NanoDrop 2000 spectrophotometer and visualized on a 1.0% agarose gel to confirm the presence of intact genomic DNA. Samples were aliquoted in nuclease-free 96-well plates and shipped to the Center for Genomics and Bioinformatics at Indiana University for WGS1 .
3
Cloning and Sequencing MYB5a Splice Variants
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Two splice variants of M. l. variegatus MYB5a, containing exons 1-2-3 and 1-2-4 respectively, were PCR-amplified using primers MYB5a-10F and MYB5a-53R (Table S1). PCR products were purified using a Genomic DNA Clean and Concentrate Kit (Zymo Research, Irvine, CA, USA), then cloned using the pGEM T-Easy kit and manufacturer's protocol (Promega, Madison, WI, USA). pGEM vector containing the desired PCR product was transformed into competent JM109 E.coli cells (Promega, Madison, WI, USA). Colonies were evaluated using blue-white screening and PCR with M13 universal primers. Inserts of the expected length were sent to Eton Bioscience (San Diego, CA, USA) for Sanger sequencing.
4
Cloning and Sequencing of MYB5a Variants
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Two splice variants of M. l. variegatus MYB5a, containing exons 1-2-3 and 1-2-4 respectively, were PCR-amplified using primers MYB5a-10F and MYB5a-53R (Supplementary Table S1). PCR products were purified using a Genomic DNA Clean and Concentrate Kit (Zymo Research, Irvine, CA, USA), then cloned using the pGEM T-Easy kit and manufacturer’s protocol (Promega, Madison, WI, USA). pGEM vector containing the desired PCR product was transformed into competent JM109 E. coli cells (Promega, Madison, WI, USA). Colonies were evaluated using blue-white screening and PCR with M13 universal primers. Inserts of the expected length were sent to Eton Bioscience (San Diego, CA, USA) for Sanger sequencing.
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