PXD009096

PXD009096 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	IsoGenie Abisko Stordalenmire LC-MSMS
Description	Large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. We investigated 1,529 microbial metagenome-assembled genomes recovered from our site to understand carbon processing in this environment. Metabolic reconstruction, supported by metatranscriptomic and metaproteomic data, revealed key populations involved in organic matter degradation, including bacteria encoding a pathway for xylose degradation only previously identified in fungi.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:45:41.800.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD009096
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Ahmed Zayed
SpeciesList	scientific name: uncultured environmental isolates; NCBI TaxID: 2042530; scientific name: Eukaryota (eucaryotes); NCBI TaxID: 2759; scientific name: environmental samples ; NCBI TaxID: 48510; scientific name: environmental samples; NCBI TaxID: 48479;
ModificationList	Carbamidomethyl
Instrument	Q Exactive

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2018-03-02 03:31:17	ID requested
1	2018-07-23 07:03:33	announced
2	2018-07-26 08:08:05	announced	Updated publication reference for PubMed record(s): 30013118.
3	2018-07-26 08:26:46	announced	Updated publication reference for PubMed record(s): 30013118.
4	2019-01-11 01:03:51	announced	Updated publication reference for PubMed record(s): 30013118.
5	2023-11-14 06:39:32	announced	2023-11-14: Updated project metadata.
⏵ 6	2024-10-22 04:45:57	announced	2024-10-22: Updated project metadata.

Publication List

S41586-018-0338-1;
10.1016/j.syapm.2018.12.003;
Woodcroft BJ, Singleton CM, Boyd JA, Evans PN, Emerson JB, Zayed AAF, Hoelzle RD, Lamberton TO, McCalley CK, Hodgkins SB, Wilson RM, Purvine SO, Nicora CD, Li C, Frolking S, Chanton JP, Crill PM, Saleska SR, Rich VI, Tyson GW, Genome-centric view of carbon processing in thawing permafrost. Nature, 560(7716):49-54(2018) [pubmed]
10.6019/PXD009096;
Martinez MA, Woodcroft BJ, Ignacio Espinoza JC, Zayed AA, Singleton CM, Boyd JA, Li YF, Purvine S, Maughan H, Hodgkins SB, Anderson D, Sederholm M, Temperton B, Bolduc B, Saleska SR, Tyson GW, Rich VI, Saleska SR, Tyson GW, Rich VI, Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov. Syst Appl Microbiol, 42(1):54-66(2019) [pubmed]
10.1038/s41586-018-0338-1;

S41586-018-0338-1;

10.1016/j.syapm.2018.12.003;

Woodcroft BJ, Singleton CM, Boyd JA, Evans PN, Emerson JB, Zayed AAF, Hoelzle RD, Lamberton TO, McCalley CK, Hodgkins SB, Wilson RM, Purvine SO, Nicora CD, Li C, Frolking S, Chanton JP, Crill PM, Saleska SR, Rich VI, Tyson GW, Genome-centric view of carbon processing in thawing permafrost. Nature, 560(7716):49-54(2018) [pubmed]

10.6019/PXD009096;

Martinez MA, Woodcroft BJ, Ignacio Espinoza JC, Zayed AA, Singleton CM, Boyd JA, Li YF, Purvine S, Maughan H, Hodgkins SB, Anderson D, Sederholm M, Temperton B, Bolduc B, Saleska SR, Tyson GW, Rich VI, Saleska SR, Tyson GW, Rich VI, Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov. Syst Appl Microbiol, 42(1):54-66(2019) [pubmed]

10.1038/s41586-018-0338-1;

Keyword List

curator keyword: Metaproteomics, Biological
submitter keyword: Permafrost,Peat

curator keyword: Metaproteomics, Biological

submitter keyword: Permafrost,Peat

Contact List

Virginia Isabel Rich
contact affiliation	Microbiology Department, The Ohio State University, United States of America
contact email	virginia.isabel.rich@gmail.com
lab head
Ahmed Zayed
contact affiliation	The Ohio State University
contact email	zayed.10@osu.edu
dataset submitter

Full Dataset Link List

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/07/PXD009096
PRIDE project URI

Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/07/PXD009096

PRIDE project URI

Repository Record List

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