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Data released on August 30, 2012

Type 2 Diabetes gut metagenome (microbiome) data from 368 Chinese samples and updated metagenome gene catalog

Cai, Z; Chen, H; Chen, W; Dai, Y; Gong, M; Guan, Y; Han, L; Jie, Z; Li, S; Li, X; Li, Z; Liang, S; Lu, D; Qin, Y; Shen, D; Sun, X; Tang, A; Wang, M; Wu, P; Wu, W; Xu, R; Yu, J; Zhang, D; Zhang, F; Zhang, M; Zhang, W; Zhang, Y; Zhang, Z; Zhong, S; Li, Y; Qin, J; Wang, J (2012): Type 2 Diabetes gut metagenome (microbiome) data from 368 Chinese samples and updated metagenome gene catalog GigaScience. http://dx.doi.org/10.5524/100036 RIS BibTeX Text

We provide data from the sequenced and analyzed gut metagenome of 368 Chinese individuals with Type 2 Diabetes (T2D) and healthy controls used in a newly developed two stage Metagenome-Wide Association Study (MWAS) aimed at identifying associations between gut microbiota and Type 2 Diabetes. The data here include the an updated metagenome gene catalog, metagenome assemblies, genetic and functional markers associated with T2D, and a novel form of marker- a Metagenomic Linkage Marker (MGL), that allows taxonomic species-level analyses without the need to identify, isolate, and culture novel bacterial species. Bacterial DNA was extracted from faecal samples and subjected to unbiased, whole-genome shotgun (WGS) sequencing using the Illumina GAIIx and HiSeq2000. In summary, 145 samples were sequenced in stage I and 378.4 Gb of paired-end (PE) sequence data were generated; 200 samples were sequenced in stage II and 830.8 Gb of PE sequence data were generated, as well as 23 additional samples for a validation study on gut-microbiota-based T2D classification. By combining MetaHIT data and our sequence data in stage I we constructed an updated human gut microbial gene catalogue, which contained 4.3 million genes suitable for studies on Chinese individuals. In this updated gene catalogue, 21.3%, 47.1% and 60.9% of genes could be assigned to known genera, KEGG and eggNOG database respectively. Taking this gene catalogue as a reference, we identified gene, KO and OG markers, respectively, which seemed to be strongly associated with T2D in our two-stage case-control study, and 47 Metagenomic Linkage Groups (MLGs). These MLGs were further assembled into different contig sets, which could provide useful genetic, functional, and taxonomic information for the relevant bacterium.

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Related manuscripts:

doi:10.1038/nature11450 (PubMed: 23023125)

Accessions (data not in GigaDB):

SRA: SRA045646
SRA: SRA050230

Metagenomic

http://gigadb.org/images/data/cropped/100036_T2D_Metagenomes.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SRS259434408170Human gut metagenome human gut metagenome Age:59
Description:A Metagenome-Wide Association Study of...
Geographic location (country and/or sea,region):Ch...
...
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SRS259435408170Human gut metagenome human gut metagenome Age:43
Description:A Metagenome-Wide Association Study of...
Geographic location (country and/or sea,region):Ch...
...
+
SRS259436408170Human gut metagenome human gut metagenome Age:46
Description:A Metagenome-Wide Association Study of...
Geographic location (country and/or sea,region):Ch...
...
+
SRS259437408170Human gut metagenome human gut metagenome Age:25
Description:A Metagenome-Wide Association Study of...
Geographic location (country and/or sea,region):Ch...
...
+
SRS259438408170Human gut metagenome human gut metagenome Age:60
Description:A Metagenome-Wide Association Study of...
Geographic location (country and/or sea,region):Ch...
...
+
SRS259439408170Human gut metagenome human gut metagenome Age:71
Description:A Metagenome-Wide Association Study of...
Geographic location (country and/or sea,region):Ch...
...
+
SRS259440408170Human gut metagenome human gut metagenome Age:62
Description:A Metagenome-Wide Association Study of...
Geographic location (country and/or sea,region):Ch...
...
+
SRS259441408170Human gut metagenome human gut metagenome Age:54
Description:A Metagenome-Wide Association Study of...
Geographic location (country and/or sea,region):Ch...
...
+
SRS259442408170Human gut metagenome human gut metagenome Age:51
Description:A Metagenome-Wide Association Study of...
Geographic location (country and/or sea,region):Ch...
...
+
SRS259443408170Human gut metagenome human gut metagenome Age:29
Description:A Metagenome-Wide Association Study of...
Geographic location (country and/or sea,region):Ch...
...
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Displaying 1-10 of 145 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
Sequence assemblyFASTA2.13 MB2012-08-30
Sequence assemblyFASTA1.39 MB2012-08-30
Sequence assemblyFASTA2.35 MB2012-08-30
Sequence assemblyFASTA856.7 KB2012-08-30
Sequence assemblyFASTA623.45 KB2012-08-30
Sequence assemblyFASTA903.24 KB2012-08-30
Sequence assemblyFASTA327.77 KB2012-08-30
Sequence assemblyFASTA3.15 MB2012-08-30
Sequence assemblyFASTA2.67 MB2012-08-30
Sequence assemblyFASTA2.68 MB2012-08-30
Displaying 1-10 of 209 File(s).

History:

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