Journal article Open Access

A communal catalogue reveals Earth's multiscale microbial diversity

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; Amir, Amnon; Navas, Jose; Kopylova, Evguenia; Ackermann, Gail

Overview

This archive contains data and results from the meta-analysis of the Earth Microbiome Project (EMP) 16S Release 1, which was published in Nature (http://doi.org/10.1038/nature24621). The files include EMP-wide study and sample metadata, observation tables and information (trees and taxonomies), alpha- and beta-diversity results, observation summaries for trading cards, and the Redbiom database at time of publication.

Files

* Study metadata
    - emp_studies.csv
* Sample metadata
    - emp_qiime_mapping_release1_20170912.tsv
    - emp_qiime_mapping_qc_filtered_20170912.tsv
    - emp_qiime_mapping_subset_10k_20170912.tsv
    - emp_qiime_mapping_subset_5k_20170912.tsv
    - emp_qiime_mapping_subset_2k_20170912.tsv
* Observation tables (.biom) and summaries (.summary.txt)
    - emp_deblur_90bp.release1.biom
    - emp_deblur_90bp.release1.summary.txt
    - emp_deblur_100bp.release1.biom
    - emp_deblur_100bp.release1.summary.txt
    - emp_deblur_150bp.release1.biom
    - emp_deblur_150bp.release1.summary.txt
    - emp_cr_gg_13_8.release1.biom
    - emp_cr_gg_13_8.release1.summary.txt
    - emp_cr_silva_16S_123.release1.biom
    - emp_cr_silva_16S_123.release1.summary.txt
    - emp_or_gg_13_8.no_sample_singletons.biom
    - emp_or_gg_13_8.no_sample_singletons.summary.txt
* Observation information (sequences, trees, taxonomies)
    - emp_observation_info_deblur.tar.gz
    - emp_observation_info_cr_gg.tar.gz
    - emp_observation_info_cr_silva.tar.gz
    - emp_observation_info_or_gg.tar.gz
* Alpha-diversity results
    - emp_alpha_div.tar.gz
* Beta-diversity results
    - emp_deblur_unifrac_dist.tar.gz
    - emp_deblur_unifrac_pc.tar.gz
    - emp_deblur_unifrac_emperor.tar.gz
    - emp_90_gg_1k_unweighted_unifrac.txt.gz
    - emp_150_gg_1k_unweighted_unifrac.txt.gz
* Observation summaries for trading cards
    - otu_summary.emp_deblur_90bp.subset_2k.rare_5000.tsv
    - otu_summary_no_chl.emp_deblur_90bp.subset_2k.rare_5000.tsv
    - emp_2k_subset_blank_stats.tsv
* Redbiom database
    - emp_redbiom.rdb

This work was supported by the John Templeton Foundation (grant ID 44000, Convergent Evolution of the Vertebrate Microbiome), the W. M. Keck Foundation (DT061413), Argonne National Laboratory (US Dept. of Energy contract DE-AC02-06CH11357), the Australian Research Council, and the Extreme Science and Engineering Discovery Environment (XSEDE, project number BIO150043), which is supported by National Science Foundation grant number ACI-1053575. We thank MO BIO Laboratories, Luca Technologies, Eppendorf, Boreal Genomics, Illumina, and Roche for in-kind support at various phases of the project.
Files (47.3 GB)
Name Size
emp_150_gg_1k_unweighted_unifrac.txt.gz
md5:ee8ed8771ff059d980c930d766f1c398 		1.8 GB Download
emp_2k_subset_blank_stats.tsv
md5:090c4241a34a01b2c607464a82591545 		48.2 MB Download
emp_90_gg_1k_unweighted_unifrac.txt.gz
md5:052414f0dc6a3fb48362e1549ea5fc95 		5.3 GB Download
emp_alpha_div.tar.gz
md5:e7723113117394d1b263bb70d5f567b8 		6.3 MB Download
emp_cr_gg_13_8.release1.biom
md5:5a08ab0811582bbc8f87a923d5c90f73 		223.1 MB Download
emp_cr_gg_13_8.release1.summary.txt
md5:f0d2093ca46ec9b68acc872eb0ad2f4b 		1.2 MB Download
emp_cr_silva_16S_123.release1.biom
md5:ba198463b2e447514db4bdf15520e1c9 		312.9 MB Download
emp_cr_silva_16S_123.release1.summary.txt
md5:9e68b3639ea527b31920fa2061aadb95 		1.2 MB Download
emp_deblur_100bp.release1.biom
md5:effaad3d0d1069b568a2eb488297035b 		286.6 MB Download
emp_deblur_100bp.release1.summary.txt
md5:7312b7dc38c766a83512c9ab53203135 		1.2 MB Download
emp_deblur_150bp.release1.biom
md5:ad414986647e0a2692679f6998923b19 		167.3 MB Download
emp_deblur_150bp.release1.summary.txt
md5:f57f801c2ee36cb37e2f6f25695a89e0 		884.2 kB Download
emp_deblur_90bp.release1.biom
md5:aee0179faa5b3f8a4499dcd1122e9213 		269.4 MB Download
emp_deblur_90bp.release1.summary.txt
md5:16a079842f14aa2ef2bfa2ea90380a0b 		1.2 MB Download
emp_deblur_unifrac_dist.tar.gz
md5:b8fb535bc57e7a7652c58fac4b82e64f 		23.9 GB Download
emp_deblur_unifrac_emperor.tar.gz
md5:109f4badf21feafd5599dbaea6706968 		29.7 MB Download
emp_deblur_unifrac_pc.tar.gz
md5:050013b9929e72d3de203233b1d3bc79 		8.8 GB Download
emp_observation_info_cr_gg.tar.gz
md5:d4347c86421cce5ae04b8070111037c1 		31.9 MB Download
emp_observation_info_cr_silva.tar.gz
md5:93b1ced0de95040cf3defe88d899be52 		78.7 MB Download
emp_observation_info_deblur.tar.gz
md5:e7fffc9cf4c8c299851c85e17ca031eb 		46.0 MB Download
emp_observation_info_or_gg.tar.gz
md5:30017a2beec94b45d715c2c2f3091b94 		346.4 MB Download
emp_or_gg_13_8.no_sample_singletons.biom
md5:674c0a9f5d84d728949f2760136f15f5 		3.1 GB Download
emp_or_gg_13_8.no_sample_singletons.summary.txt
md5:d993c7efc5d8185b8432ccf051d43d48 		1.3 MB Download
emp_qiime_mapping_qc_filtered_20170912.tsv
md5:232e5a6b1d85ad9b274585d3391c7142 		19.1 MB Download
emp_qiime_mapping_release1_20170912.tsv
md5:66ffe99e81c619e9a6056b72c1e6661d 		21.9 MB Download
emp_qiime_mapping_subset_10k_20170912.tsv
md5:e3c56567c54e826d89637f9ad37eb130 		7.9 MB Download
emp_qiime_mapping_subset_2k_20170912.tsv
md5:25cf231f596e9d0543f61b2985baed82 		1.6 MB Download
emp_qiime_mapping_subset_5k_20170912.tsv
md5:a28d2796b6317cd2ec9c0761e20f9ad1 		4.0 MB Download
emp_redbiom.rdb
md5:a2c03084ad8fd8eac87675ac1914c389 		2.5 GB Download
emp_studies.csv
md5:c3b91a45b3303d0ec7f21e6adedbe220 		68.6 kB Download
otu_summary.emp_deblur_90bp.subset_2k.rare_5000.tsv
md5:584ea257f98a6c7344510049c5620cc3 		54.0 MB Download
otu_summary_no_chl.emp_deblur_90bp.subset_2k.rare_5000.tsv
md5:3c61c50cbe161e196b45e3679b87b925 		55.6 MB Download
README.md
md5:87d6165220eddd0725aff9f7e25c0e73 		1.8 kB Download
8,174
11,823
views
downloads
All versions This version
Views 8,1748,177
Downloads 11,82311,825
Data volume 65.1 TB65.1 TB
Unique views 7,5537,556
Unique downloads 3,3503,352
More info on how stats are collected.
Indexed in
Publication date:
November 1, 2017
DOI:
10.5281/zenodo.890000

Zenodo DOI Badge

DOI 

10.5281/zenodo.890000

Markdown 

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.890000.svg)](https://doi.org/10.5281/zenodo.890000)

reStructedText 

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.890000.svg
   :target: https://doi.org/10.5281/zenodo.890000

HTML 

<a href="https://doi.org/10.5281/zenodo.890000"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.890000.svg" alt="DOI"></a>

Image URL 

https://zenodo.org/badge/DOI/10.5281/zenodo.890000.svg

Target URL 

https://doi.org/10.5281/zenodo.890000

Keyword(s):
microbiome amplicon sequencing environmental microbiology
Published in:
Nature:.
Related identifiers:
Cited by
License (for files):
Creative Commons Attribution 4.0 International

Versions

Version 1 10.5281/zenodo.890000 Nov 1, 2017
Cite all versions? You can cite all versions by using the DOI 10.5281/zenodo.889999. This DOI represents all versions, and will always resolve to the latest one. Read more.

Share

Cite as

Export