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8 protocols using nanodrop one c microvolume spectrophotometer

1

Fecal Microbiome Analysis for Canine Cognition

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Fecal samples were collected on the memory test day or a few days apart (N = 10 days average), by putting a sterile P1000 pipettor tip (upside-down) into the feces immediately after the dogs defecated. The fecal samples were placed in sterile 1.5mL Eppendorf tubes and stored immediately in −80 C freezer. For microbial DNA purification, ∼200 mg fecal sample was homogenized by the PowerLyzer24 instrument (Qiagen, Germantown, MD, USA) in bead-containing tubes provided in the AllPrep PowerFecal DNA/RNA kit (Qiagen, Germantown, MD, USA), and DNA samples were extracted according to the manufacturer’s protocol. DNA concentrations were measured on a Qubit Fluorometer (Invitrogen, Carlsbad, CA, USA), and A260/A280 absorption ratios were assessed using a NanoDrop One C Microvolume Spectrophotometer (Thermo Scientific, Waltham, MA, USA). The size distribution was checked on TapeStation 4200 using Genomic ScreenTape (Agilent Technologies, Santa Clara, CA, USA).
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2

Microbial DNA Extraction and Sequencing

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The Qiagen Allprep PowerFecal DNA/RNA kit (Qiagen, Redwood City, CA, USA) was used for microbial DNA extraction. For each cat, the weight of fecal specimens was measured (Table 2) before being placed into a Microbial Lysis Tube for homogenization using a PowerLyzer24 instrument (Qiagen, Redwood City, CA, USA). DNA extraction procedures were conducted for all fecal samples in the same batch to minimize technical variability. The DNA concentrations were measured using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA), and the A260/A280 absorption ratios were determined with a NanoDrop One C Microvolume Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). 500 ng of DNA from each sample was fragmented into 500-bp fragments using an M220 Focused-ultrasonicator (Covaris, Woburn, MA, USA). The WGS metagenomic libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA). TapeStation 4,200 (Agilent Technologies, Santa Clara, CA, USA) was utilized to evaluate the library size distributions. Subsequently, the final libraries were quantified using qPCR before being sequenced on an Illumina NovaSeq6000 sequencing platform in 150-bp paired-end mode by Novogene Corporation Inc. in Sacramento, CA, USA.
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3

Metagenomic DNA extraction and sequencing from feline feces

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Two fecal samples were collected from each cat using a fecal loop with and without lubrication (N = 14 total; Supplementary Table S1) (32 (link)). At least 200 mg feces were used for DNA extraction by Qiagen Allprep PowerFecal DNA/RNA kit (Qiagen, MD), following the protocols provided by the manufacturer. During DNA extraction, fecal samples were homogenized by the Qiagen PowerLyzer24 instrument (Qiagen, MD) to achieve homogeneous results. The extracted DNA concentrations were measured by the Qubit 3 Fluorometer (Invitrogen, CA), and A260/A280 absorption ratios were assessed using the NanoDrop One C Microvolume Spectrophotometer (Thermo Fisher Scientific, MA). DNA fragmentation was performed by M220 Focused-ultrasonicator (Covaris, MA) on 1.5–2 μg of DNA for each sample to achieve fragmented DNA of ~500 bp. NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, MA) was used to construct WGS metagenomic sequencing libraries using the fragmented DNA. Final library concentrations and size distributions were measured by LabChip GX Touch HT Nucleic Acid Analyzer (PerkinElmer, MA) before being sequenced on an Illumina NovaSeq6000 sequencing machine on the 150-bp paired-end mode at the Genomics Service Laboratory at the HudsonAlpha Institute for Biotechnology (Huntsville, AL).
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4

Serum Hormones and Protein Quantification

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For the measurement of serum corticosterone and protein concentration, the animals were decapitated 30 min after icv. treatment. For the assessment of serum LH, decapitation was performed 15 min after icv. treatment. Trunk blood was collected into test tubes and left at room temperature for 30 min to clot, then it was centrifuged for 10 min at 3500 rpm. The samples were stored at −80 °C until the assays were performed. Serum corticosterone concentration was measured using a competitive corticosterone ELISA kit (Cayman Chemical, Ann Arbor, MI, USA), according to the manufacturer’s instruction. Serum LH concentration was determined using a sandwich LH ELISA kit (Wuhan Xinquidi Biological Technology Co., Wuhan, China), according to the manufacturer’s instructions. The Pierce Coomassie (Bradford) Protein Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA) was used, according to the manufacturer’s instructions for the measurement of total serum protein concentration. The absorbance was measured at 595 nm with a NanoDrop OneC microvolume spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).
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5

Sperm RNA Extraction and Sequencing

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Three biological replicates of fresh-frozen sperm samples and cryopreserved sperm samples were used for RNA extraction, which underwent the same thawing procedure (40 °C water bath for 20 s). To achieve high reproducibility, the sperm samples were homogenized using a PowerLyzer24 instrument (Qiagen, Redwood City, CA, USA). Total RNA was extracted using AllPrep DNA/RNA Kit (Qiagen, Redwood City, CA, USA) following the manufacturer’s instructions. RNA concentrations were measured with the NanoDrop OneC Microvolume Spectrophotometer (Thermo Scientific, Waltham, MA, USA). Evaluation of RNA quality was conducted using the LabChip GX Touch HT (PerkinElmer, Hopkinton, MA, USA). RNA-seq library construction was performed following the procedure described in our previous publication [96 (link)] with 500 ng of total RNA input. The size distributions of cDNA libraries were checked using the TapeStation 4200 D1000 ScreenTape (Agilent Technologies, Santa Clara, CA, USA), and library concentrations were determined by a Qubit 3.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). The libraries were commercially sequenced on the Illumina NovaSeq 6000 platform with a 2 × 150 Paired-End configuration at Novogene (Novogene Corporation Inc., Sacramento, CA, USA).
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6

Fecal DNA Extraction for Microbiome Analysis

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Genomic DNA samples were extracted from 200 mg fecal samples using the Allprep PowerFecal DNA/RNA kit (Qiagen, Redwood City, California) according to the manufacturer's protocols. To reduce technical variability, the homogenization step was performed for all fecal samples in the same batch using a PowerLyzer24 instrument (Qiagen, Redwood City, California). DNA concentrations were measured by a Qubit 3.0 Fluorometer (Thermo Fisher Scientific, Waltham, Massachusetts), and the A260/A280 absorption ratios were assessed by a NanoDrop One C Microvolume Spectrophotometer (Thermo Scientific, Waltham, Massachusetts).
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7

Fecal Sampling and Gut Microbiome Analysis

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Fecal samples were collected under sedation immediately after blood collection to prevent interference of epinephrine-mediated hyperglycemia (Table S1). Plastic fecal loops were coated with mineral oil and inserted into the rectum and descending colon of the cats until an adequate amount of feces was collected. The samples in this study reflect the fecal composition of the rectum and descending colon, which is representative of the lower gut. We referred to the microbiota characterized in the fecal samples in this research as cat gut microbiota.
Genomic DNA samples were extracted from 200 mg fecal samples using the Qiagen Allprep PowerFecal DNA/RNA kit (Qiagen, MD) following the manufacturer’s protocols. To achieve homogeneous results, the homogenization step was performed by the Qiagen PowerLyzer24 instrument (Qiagen, MD) in the same batch. DNA and total RNA concentrations were measured by a Qubit 3 Fluorometer (Invitrogen, CA), and the A260/A280 absorption ratios were assessed using a NanoDrop One C Microvolume Spectrophotometer (Thermo Fisher Scientific, MA).
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8

DNA Extraction and Whole Genome Sequencing

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Phage DNA was extracted using Invitrogen’s PureLink Viral RNA/DNA Extraction Kit (catalog #12280-050) using the manufacturer’s protocol, and bacterial DNA was extracted using Promega’s Wizard Genomic DNA Purification Kit (catalog #A1120) using the manufacturer’s protocol. The extracted DNA was quantified on a ThermoFisher’s NanoDrop OneC Microvolume Spectrophotometer (catalog #ND-ONE-W). Samples were sent to the Microbial Genome Sequencing Center in Pittsburgh, PA, USA, for whole genome sequencing on the Illumina NextSeq 2000 platform. FASTAq files received from the Microbial Genome Sequencing Center were analyzed using Geneious Prime version 2022.0.1.
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