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What was your extracted [DNA]? triplicate PCRs or just one reaction per sample? Have you tried reextracting that sample or at least reamplifying the extract you have? I haven't worked on fish, but I'd expect an animal that has just mycoplasma in their gut to be fairly sick looking. I'd be surprised if the issue is in the sequencer when you're getting millions of reads (regardless if they were multiplexed with samples that were pure mycoplasma, you shouldn't get that much index jumping). I'd focus on wet lab contamination.
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Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct. -
Triplicate pcr's - a lot of studies pubkished recently on fish gut microbiome are finding mycoplasma, so I'm not sure if it's contamination. Plus we tested samples of the reagents as neg controls too and no myco. We did find a great diversity of otus too not just pure myco.
If 24 samples on one miseq flow cell, should produce over 500k reads per sample no? Considering illumina expects 100k per sample if 96 samples are run, as per their protocol?Comment
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Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM -
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...03-22-2024, 06:39 AM
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