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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
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    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    screencap from Amundson and Wilkins subsurface microbiome video
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    Boosting Small Molecule Production in Super “Soup”
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    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
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    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
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User Programs
Home › User Programs › User Support › Sequencing Sample Overview › Plate Preparation Guidelines

Plate Preparation Guidelines

For submission of materials in 96-well plate format, the JGI requires that investigators adhere to the guidelines outlined below in addition to the material-specific sample requirements described on our website.

The following library types are supported in plate format:

DNA:

  • Illumina 300 bp fragment libraries (typically used for microbial minimal drafts and metagenomes)
  • Nextera 300 bp fragment libraries (typically used for single cell and single particle sort projects)
  • Illumina 500 bp fragment libraries (typically used for resequencing projects and fungal minimal drafts)
  • Illumina Bisulfite libraries (5mC detection)

RNA:

  • PolyA-selected libraries
  • rRNA-depleted libraries
  • Eukaryotic smRNA libraries

For all other library types, please ship your samples in tubes.  If you are unsure of the correct format, please discuss with your Project Manager.

Sample Preparation

  • If you are shipping 22 or more samples at one time from the products listed above, you should submit in 96-well plate format.
  • A maximum of 46 samples per plate may be submitted for eukaryotic smRNA. For all other library types, a maximum of 92 samples per plate may be submitted.
  • We recommend sending DNA samples in low EDTA TE buffer (molecular biology grade, DNase/RNase/protease-free, such as this one from VWR), and RNA samples in DNase-treated and nuclease-free water, where they are most stable.
  • You must assess the quality of at least 10% of samples prior to submission.  JGI’s recommended protocols are below.

Genomic DNA QC protocol | Total RNA QC protocol | Small RNA QC Protocol

Plate Preparation

  • We require the use of the prelableled, barcoded plates provided by the JGI.
  • Leave the corner wells (A1, A12, H1 and H12) EMPTY.
  • Fill the plate by column, placing the first sample in well B1 (Column 1 B-G, then Column 2 A-H, Column 3 A-H, etc.).  See diagram below.

  • The mass should be consistent across all samples in the plate and within the ranges below.  If you are unable to provide sufficient mass, please contact your Project Manager, as alternate protocols may be available (though typically at much lower throughput).
  • Leave unused wells empty.
  • After placing samples in the plate, seal with the new sealer contained within the shipment.
Library type Requested mass (ng)* Volume range (ul) Concentration range (ng/ul) DNAse treatment required Minimum # samples per plate Maximum # samples per plate
Illumina fragment (400 bp) 500 25-150 10-1000 No 22 92
Nextera 10 25-150 0.2-1000 No 22 92
Illumina Bisulfite library 3000 25-150 10-1000 No 22 92
Eukaryotic RNA (polyA selection) – standard 3000 25-150 50-1000 Yes 22 92
Eukaryotic RNA (polyA selection) – low input 300 25-150 10-1000 Yes 22 92
Prokaryotic RNA (rRNA depletion) – low input 300 25-150 10-1000 Yes 22 92
Eukaryotic smRNA 4000 25-150 167-1000 Yes 22 46

Plate Naming

  • Plate name must be unique and descriptive, and <21 characters in length.
  • “Plate Label” is the field in the metadata submission tool in which you will enter this information.
  • Prior to shipment, confirm that the plate label information submitted with the metadata matches the physical label on the plate.
  • Mismatched or improperly labeled materials will be returned to the shipper.

Examples:

  • 504675_RNA.1
  • Smith_DNA300_5

If you are having trouble determining a unique name for your plate, please consult your Project Manager.

Plate Processing

  • JGI’s library construction protocols are optimized for use on full plates of samples. Samples from your plate may be combined with samples from other plates, at JGI’s discretion.

Last update: 2/10/22

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