hmgc1 subgingival plaque (Collection)

Subset Collection:

hmgc1

Collection (Entity type)

Project:

HHS

Project (Entity type)

Dcc Asset:

datapackage.zip

Processed File (Entity type)

Dcc:

HMP

DCC (Entity type)

Has Time Series Data:false

Description:This collection contains a non-redundant catalog of bacterial genes from subgingival_plaque samples. This was done by clustering the gene indices (refer "hmgi1_subgingival_plaque" collection), using the same identity parameter used by the Metahit project to cluster their human intestinal tract data (Qin et al, 2010. Nature, 464:59). Genes were compared at a 95% identity cut-off and those overlapping were considered redundant and removed. Attention: the gene counts available here differ from what was originally reported in the publication. This is due to the fact that samples that did not pass our assembly QC had not been removed prior to initial clustering. Clustering has been rerun and the data is now accurate.

Abbreviation:hmgc1_subgingival_plaque

Results found

Linked to

	Label	Description
	hmgc1 Collection (Entity type)	Clustered gene index: This collection contains a non-redundant catalog of bacterial genes by body si...
	HHS 763577454 Subject (Entity type)	A subject produced as part of the HHS project
	subgingival plaque nr nuc.fasta.bz2 File (Entity type)	A 80.4 MB file from HMP produced from OBI:0002623 as part of the HHS project
	SRS014691 Biosample (Entity type)	A biosample from HMP produced as part of the HHS project
	SRS013950 Biosample (Entity type)	A biosample from HMP produced as part of the HHS project
	SRS019129 Biosample (Entity type)	A biosample from HMP produced as part of the HHS project
	SRS014477 Biosample (Entity type)	A biosample from HMP produced as part of the HHS project
	SRS014107 Biosample (Entity type)	A biosample from HMP produced as part of the HHS project
	HHS 764042746 Subject (Entity type)	A subject from HMP produced as part of the HHS project
	subgingival plaque nr.fasta.bz2 File (Entity type)	A 52.5 MB file from HMP produced from OBI:0002623 as part of the HHS project

hmgc1

Collection (Entity type)

Clustered gene index: This collection contains a non-redundant catalog of bacterial genes by body si...

HHS 763577454

Subject (Entity type)

A subject produced as part of the HHS project

subgingival plaque nr nuc.fasta.bz2

File (Entity type)

A 80.4 MB file from HMP produced from OBI:0002623 as part of the HHS project

SRS014691

Biosample (Entity type)