Emp Sample Submission Guide Pfqdjmw

This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution,

and reproduction in any medium, provided the original author and source are credited

EMP Sample Submission Guide

Luke Thompson,Gail Ackermann,Greg Humphrey,Jack Gilbert,Janet Jansson,Rob Knight

This protocol was designed for collaborators with the Earth Microbiome Project to contribute

samples in a standardized fashion. Raw, frozen samples are submitted in individually labeled

tubes, 10 aliquots (identical replicates) per sample. Please note that unsolicited samples cannot

Samples for this study will ideally meet the following criteria:

Fresh or frozen sample (no preservatives) in ~10 aliquots

Metadata well characterized

Large proportion of unmapped diversity in at least some samples

Non-human-associated and non-human-perturbed samples will be given priority

Shipping Guidelines

For non-soil samples only (e.g., feces, sediments, biofilms, organic material, water filters), no

special permits should be necessary. However, material transfer agreements (MTAs) may be required,

regulated, the permit is not needed.

The PPQ Form 550 Black/White Label (sticker) must be affixed to the outside of the shipment for

any soils shipping from outside the USA, Guam, Hawaii, Puerto Rico, or the US Virgin Islands.

Samples should be shipped with FedEx overnight (or DHL for international shipments). Soil

samples must be shipped to the permit holder.

This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution,

and reproduction in any medium, provided the original author and source are credited

MTAs may also be required by the sending and receiving institutions, and these should be

agreed upon as early as possible.

BD SWUBE™ collection and transport system 281130 by Bd

Millipore Express PLUS Membrane Filter, polyethersulfone, Hydrophilic, 0.22 µm, 47 mm

Step 1.

Samples should be collected fresh and split into 10 aliquots and then frozen, or collected and frozen

and subsequently split into 10 aliquots with minimal perturbation.

Do not use any buffers or solutions to preserve your samples. Do not use RNAlater. Ethanol

(50-95%) is acceptable. Aliquot size should be sufficient to yield 10-100 ng genomic DNA, which is

approximately 107 to 108 cells. For low-biomass samples, such as certain water samples and biofilms,

please contact us.

Procedures specific to sample types

Step 2.

-80 °C Additional info: Storage

REAGENTS

sterile, 100 pcs./bag 72.694.005 by Sarstedt

Step 4 - Bulk unaltered (Examples: soil, sediment, feces).

This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution,

and reproduction in any medium, provided the original author and source are credited

To track the provenance of these aliquots, we employ the following QR barcoding scheme:

Step 3 - Bulk fractionated (Examples: sponges, corals, turbid water).

Fractionate the sample as appropriate for your sample type. Split into 10 2-mL screw-cap bead

beater tubes, ideally with at least 200 mg biomass, flash freeze in liquid nitrogen (if possible), and

store at -80 °C (or -20 °C).

TEMPERATURE

-80 °C Additional info: Storage

REAGENTS

sterile, 100 pcs./bag 72.694.005 by Sarstedt

Other naming conventions are acceptable, but please make sure the names match those in the

metadata CSV file.

Please do not number the aliquots; you should submit 10 identically labeled aliquots for each

Procedures specific to sample types

Step 3 - Swabs (Examples: biofilms, feces).

Take 10 replicate swabs using 5 BD SWUBETM dual cotton swabs with wooden stick and screw cap.

Place cap on swabs and store in -80 °C (or -20 °C).

TEMPERATURE

This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution,

and reproduction in any medium, provided the original author and source are credited

-80 °C Additional info: Storage

sequential number: “Jones99.soil.1”.

This is the default sample numbering system used in the metadata template (see in Guidelines).

Other naming conventions are acceptable, but please make sure the names match those in the

metadata CSV file.

Please do not number the aliquots; you should submit 10 identically labeled aliquots for each

Procedures specific to sample types

Step 3 - Filters (Example: water).

GPWP04700 by Millipore

sterile, 100 pcs./bag 72.694.005 by Sarstedt

Step 4 - Filters (Example: water).

To track the provenance of these aliquots, we employ the following QR barcoding scheme:

This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution,

and reproduction in any medium, provided the original author and source are credited

Step 3.

Place filters in micro centrifuge tubes or cry-vials, flash freeze in liquid nitrogen (if possible), and store

at -80 °C (or -20 °C).

-80 °C Additional info: Storage

Please refer to the SDS (Safety Data Sheet) for safety and hazard information.