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text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2059_533_Arch


text: public

text: Denmark

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text: Cattle rumen microbiota for IC-2059_267_Bact


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text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_471_Arch


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_493_Arch


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_559_Arch


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_484_Arch


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_542_Arch


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_534_Arch


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_490_Arch


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_470_Arch


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_489_Arch


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text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_497_Arch


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_507_Arch


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text: Denmark

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text: Cattle rumen microbiota for IC-2059_280_Bact


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text: Denmark

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text: stomach metagenome

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text: Center for Quantitative Genetics and Genomics

text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2059_311_Bact


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_289_Bact


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_347_Bact


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_482_Arch


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text: Denmark

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text: Cattle rumen microbiota for IC-2059_302_Bact


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text: Denmark

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text: Cattle rumen microbiota for IC-2059_300_Bact


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_503_Arch


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text: Denmark

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text: Cattle rumen microbiota for IC-2059_277_Bact


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text: Denmark

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text: Denmark

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text: Cattle rumen microbiota for IC-2059_310_Bact


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text: Denmark

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text: Cattle rumen microbiota for IC-2059_313_Bact


text: public

text: Denmark

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text: Cattle rumen microbiota for IC-2059_514_Arch


text: public

text: Denmark

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text: Cattle rumen microbiota for IC-2059_476_Arch


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text: Denmark

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text: Cattle rumen microbiota for IC-2059_279_Bact


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_508_Arch


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text: Center for Quantitative Genetics and Genomics

text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2059_502_Arch


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_265_Bact


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_483_Arch


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_535_Arch


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_259_Bact


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_531_Arch


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text: Denmark

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text: Cattle rumen microbiota for IC-2059_273_Bact


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_296_Bact


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_540_Arch


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_527_Arch


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_352_Bact


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text: Denmark

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text: Cattle rumen microbiota for IC-2059_301_Bact


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_501_Arch


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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_565_Arch


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text: Cattle rumen microbiota for IC-2059_294_Bact


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text: Cattle rumen microbiota for IC-2059_526_Arch


text: Center for Quantitative Genetics and Genomics

text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2059_356_Bact


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_462_Arch


text: public

text: Denmark

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text: stomach metagenome

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text: Denmark

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text: stomach metagenome

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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_485_Arch


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text: Denmark

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text: Cattle rumen microbiota for IC-2059_288_Bact


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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_467_Arch


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text: Cattle rumen microbiota for IC-2059_344_Bact


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text: Denmark

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text: public

text: Denmark

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text: Cattle rumen microbiota for IC-2059_353_Bact


text: public

text: Denmark

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text: Denmark

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text: Cattle rumen microbiota for IC-2059_547_Arch


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_343_Bact


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text: Denmark

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text: Cattle rumen microbiota for IC-2059_263_Bact


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text: Denmark

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text: Denmark

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text: Center for Quantitative Genetics and Genomics

text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_552_Arch


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_309_Bact


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_537_Arch


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text: Denmark

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text: stomach metagenome

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text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_479_Arch


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_528_Arch


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_492_Arch


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Denmark

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text: Cattle rumen microbiota for IC-2059_266_Bact


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_481_Arch


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_494_Arch


text: public

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text: stomach metagenome

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text: Denmark

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text: Cattle rumen microbiota for IC-2059_475_Arch


text: public

text: Denmark

text: Midtjylland

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text: Center for Quantitative Genetics and Genomics

text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_341_Bact


text: public

text: Denmark

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text: Cattle rumen microbiota for IC-2059_363_Bact


text: public

text: Denmark

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text: Cattle rumen microbiota for IC-2059_569_Arch


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_495_Arch


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_516_Arch


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2059_295_Bact


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_14b_lib38058


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_8a_lib38045


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_33b_lib38096


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_35b_lib38100


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_1a_lib38033


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_2b_lib38036


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_16a_lib38061


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_14a_lib38057


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_43a_lib38115


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_3a_lib38037


text: Center for Quantitative Genetics and Genomics

text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_4a_lib38039


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_29b_lib38088


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_9a_lib38047


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_34a_lib38097


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_16b_lib38062


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_6a_lib38041


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_37b_lib38104


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_18b_lib38066


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_36a_lib38101


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_10b_lib38050


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_44a_lib38117


text: public

text: Denmark

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text: Cattle rumen microbiota for IC-2034_32b_lib38094


text: public

text: Denmark

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text: Cattle rumen microbiota for IC-2034_35a_lib38099


text: public

text: Denmark

text: Midtjylland

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text: Cattle rumen microbiota for IC-2034_21a_lib38071


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_2a_lib38035


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_47a_lib38123


text: Center for Quantitative Genetics and Genomics

text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_30a_lib38089


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_26b_lib38082


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_38b_lib38106


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_8b_lib38046


text: public

text: Denmark

text: Midtjylland

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text: Cattle rumen microbiota for IC-2034_49a_lib38127


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_20b_lib38070


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_25b_lib38080


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_46a_lib38121


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_15a_lib38059


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_7a_lib38043


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_24b_lib38078


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_19a_lib38067


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_28b_lib38086


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_18a_lib38065


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_22a_lib38073


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_11b_lib38052


text: Center for Quantitative Genetics and Genomics

text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_27a_lib38083


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_17a_lib38063


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_47b_lib38124


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_45b_lib38120


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_12a_lib38053


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_15b_lib38060


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_43b_lib38116


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_25a_lib38079


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_37a_lib38103


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_48b_lib38126


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_33a_lib38095


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_9b_lib38048


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_11a_lib38051


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_34b_lib38098


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_24a_lib38077


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_26a_lib38081


text: Center for Quantitative Genetics and Genomics

text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_3b_lib38038


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_27b_lib38084


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_12b_lib38054


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_40a_lib38109


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_6b_lib38042


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_23b_lib38076


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_30b_lib38090


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_31a_lib38091


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_22b_lib38074


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_1b_lib38034


text: public

text: Denmark

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text: Cattle rumen microbiota for IC-2034_29a_lib38087


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_17b_lib38064


text: public

text: Denmark

text: Midtjylland

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text: Cattle rumen microbiota for IC-2034_38a_lib38105


text: public

text: Denmark

text: Midtjylland

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text: Cattle rumen microbiota for IC-2034_40b_lib38110


text: public

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text: Cattle rumen microbiota for IC-2034_23a_lib38075


text: public

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text: stomach metagenome

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_32a_lib38093


text: Center for Quantitative Genetics and Genomics

text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_31b_lib38092


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_13a_lib38055


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_42b_lib38114


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_42a_lib38113


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_39a_lib38107


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_45a_lib38119


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_48a_lib38125


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_41a_lib38111


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_46b_lib38122


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_13b_lib38056


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

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text: stomach fluid

text: Cattle rumen microbiota for IC-2034_44b_lib38118


text: public

text: Denmark

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text: Cattle rumen microbiota for IC-2034_7b_lib38044


text: public

text: Denmark

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text: stomach metagenome

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text: Cattle rumen microbiota for IC-2034_20a_lib38069


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_19b_lib38068


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_4b_lib38040


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_41b_lib38112


text: Center for Quantitative Genetics and Genomics

text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_21b_lib38072


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_10a_lib38049


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_39b_lib38108


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_36b_lib38102


text: public

text: Denmark

text: Midtjylland

text: stomach metagenome

text: stomach metagenome

text: stomach fluid

text: Cattle rumen microbiota for IC-2034_49b_lib38128


text: public

text: Denmark

text: Midtjylland

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text: Cattle rumen microbiota for IC-2034_28a_lib38085


text: EMBL

text: public

characteristic: collection date

text: Altered gut microbiome composition has been associated with many human diseases. However, microbiome-disease association studies have not always reported consistent results, creating an increasing need for cross-study comparisons. Here we present a meta-analysis of five faecal shotgun metagenomic studies of colorectal cancer (CRC) that are diverse in geographic sampling range and metagenomic data generation. We find a core of 30 species to be differentially abundant in CRC metagenomes (stringent FDR of 1E-05) including 8 species without genomic reference. Metagenomic classification models trained to detect CRC on one study generally maintained similar accuracy when applied to other studies. When combining training data across four studies, average accuracy on the fifth, held-out study was 0.83 (area under the receiver operating characteristic curve). These classifiers were CRC-specific as they maintained the expected false positive rate on other diseases. Functional metagenomic analysis uncovered an enrichment of amino acid and mucin degradation pathways in CRC metagenomes concomitant with a depletion of carbohydrate degradation, in line with established dietary CRC risk factors. We moreover found a strong enrichment of secondary bile acid conversion genes in CRC metagenomes suggesting a metabolic link between CRC-associated gut microbes and a high-risk diet rich in fat and red meat. Taken together, our meta-analysis establishes predictive taxonomic and functional metagenomic signatures for CRC that are robust to technical and biological variation providing further support for the development of microbiome-based diagnostic tests.

characteristic: description

text: Feces

characteristic: environment (biome)

text: Feces

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: Germany

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

unit: year

characteristic: host age

characteristic: host body mass index

text: stool

characteristic: host body product

text: male

characteristic: host sex

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: human gut metagenome

characteristic: project name

text: human gut metagenome

text: Illumina HiSeq

characteristic: sequencing method

text: Meta-analysis of faecal metagenomes reveals global microbial signatures that are specific for colorectal cancer


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Feces

text: Feces

text: stool

text: Germany

characteristic: geographic location (country and/or sea)

text: stool

text: female

text: human-gut

text: metagenome

text: human gut metagenome

characteristic: organism

text: human gut metagenome

text: Illumina HiSeq


text: public

tag: Namespace:Environment Centre Wales (Bangor University)

characteristic: collection date

text: GMEP 18S sample collected with co-located with 16S, ITS1, and soil data

characteristic: description

text: temperate grassland biome

characteristic: environment (biome)

text: Soil

characteristic: environment (material)

text: United Kingdom

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

text: soil metagenome

text: The Glastir Monitoring & Evaluation Programme - sequencing data from microbiology cores of years 1 and 2 (2013-2014) using the 16S marker gene.

text: soil metagenome

text: Illumina MiSeq

text: soil

characteristic: soil environmental package

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Environment Centre Wales (Bangor University)

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: temperate grassland biome

text: Soil

text: United Kingdom

text: mimarks-survey

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: soil metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: soil


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: forest biome

characteristic: environment (biome)

text: Soil

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: mimarks-survey

text: soil metagenome

characteristic: organism

text: soil metagenome

text: Illumina MiSeq

text: soil


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: temperate shrubland biome

text: Soil

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

text: soil metagenome

text: soil metagenome

text: Illumina MiSeq

text: soil

characteristic: soil environmental package

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: cropland biome

text: Soil

text: United Kingdom

text: mimarks-survey

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: soil metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: soil


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: Soil

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: mimarks-survey

text: soil metagenome

characteristic: organism

text: soil metagenome

text: Illumina MiSeq

text: soil


characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:School of Environmental Science and Engineering in Tianjin University

text: Bacteria

characteristic: environment (biome)

text: anaerobic sludge digestion

characteristic: environment (feature)

text: wastewater sludge

characteristic: environment (material)

text: China

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: sludge granule bacterium 1

text: sludge granule bacterium 1

text: 16s RNA Amplicon Sequencing

text: Analysis of the Bacterial Community Structure

characteristic: title

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: External Id

text: School of Environmental Science and Engineering in Tianjin University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Bacteria

text: anaerobic sludge digestion

text: wastewater sludge

text: China

text: metagenome

characteristic: investigation type

text: sludge granule bacterium 1

characteristic: project name

text: sludge granule bacterium 1

text: 16s RNA Amplicon Sequencing

characteristic: sequencing method

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: dongjuan

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: drinking water

text: premise plumbing

text: water

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: metagenome

text: metagenome

characteristic: organism

text: metagenome

text: Illumina HiSeq

text: Hot water metagenomics

text: water

characteristic: water environmental package


AFAAObiofilm

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Beijing University of Technology

text: public

text: AFAAObiofilm

tag: Namespace:Beijing University of Technology

text: China

text: 39.9 N

characteristic: geographic location (latitude)

text: 116.3 E

characteristic: geographic location (longitude)

text: metagenome

text: metagenome

text: metagenome

text: biofilm

characteristic: sewage type

text: AFAAObiofilm

characteristic: title


AFAAOfloc

text: Beijing University of Technology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: AFAAOfloc

text: China

text: 39.9 N

text: 116.3 E

text: metagenome

characteristic: investigation type

text: metagenome

text: metagenome

text: floc

text: AFAAOfloc


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-7093:Au-COOH_20 nanometer_15ug/mL_r1

tag: Namespace:Division of Chemical Biology,  Department of Biology and Biological Engineering

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: monocyte

characteristic: cell type

text: human

characteristic: common name

text: Protocols: The undifferentiated monocytic THP.1 cell line was purchased from ATCC® (#TIB202). The cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 100 U/mL penicillin, 100 μg/mL streptomycin, and 0.05 mM β-mercaptoethanol. The cell density was strictly kept between 0.1 to 2 million cells/mL. Undifferentiated THP.1 cells (1 milion cells per condition) were exposed to the 6 Au NPs (two diameters 5 and 20 nm, and three functional surface groups -NR3+, -COOH and -PEG) at different doses for 6 h followed by RNA extraction. Based on the preliminary cytotoxicity screening we have determined the doses inducing 10% of cell death for Au-5-NH2 (EC10= 27 µg/mL) and Au-20-NH2 (EC10= 4 µg/mL). The EC10 values for the 4 other NPs were not determined (EC10> 100 µg/mL). In this pilot study, cells were exposed: (1) to the three Au-5(-NH2/-COOH/-PEG) NPs at a concentration of 27 µg/mL (corresponding to the individual EC10 dose for the set of 5 nm size NPs), (2) to the three Au-20(-NH2/-COOH/-PEG) NPs at a concentration of 4 µg/mL (corresponding to the individual EC10 dose for the set of 20 nm size NPs) or (3) to all the Au-5 and Au-20 (-NH2/-COOH/-PEG) at a concentration of 15 µg/mL (corresponding to the average EC10 dose). The control used was cells incubated with culture media only. Each condition was performed in triplicate. After exposure, the cells were washed twice with ice-cold PBS by centrifugation 300 g, 5 min at 4°C. The cells were lysed with 350 µL of Buffer RLT Plus, supplemented with β-mercaptoethanol, from the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). Samples were stored at -80°C before RNA/DNA extraction. Qiagen protocol was strictly applied. At the end of the procedure, RNA was eluted at once with 30 µL of RNAse free water. Aliquots of 3 µL of each RNA samples were prepared for quality analysis. The concentrations of total RNA were measured with Nanodrop spectrophotometer and Qbit fluorescence. The RNA samples were carefully labelled and stored at -80°C prior to sequencing. Bulk-RNA transcriptome analysis was performed by the STRT RNA-seq method (PMID: 22481528) with minor modifications (PMID: 26874359). Briefly, ten nanogram of high-quality input RNA was converted to cDNA and amplified to form an Illumina-compatible 46-plex library. ERCC RNA Spike-In Mix 1 (cat. 4456740; ThermoScientific) was used in 1000X dilution. In total, 25 PCR cycles were used, but as six base-pair unique molecular identifiers (UMIs) were applied, only the absolute number of unique reads was calculated per analyzed sample.

characteristic: description

text: acute monocytic leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: Au-COOH_20 nanometer_15ug/mL_r1


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Division of Chemical Biology, Department of Biology and Biological Engineering

text: public

text: E-MTAB-7093:Au-COOH_20 nanometer_15ug/mL_r2

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-COOH_20 nanometer_15ug/mL_r2

characteristic: title


characteristic: INSDC center name

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text: public

characteristic: INSDC status

text: E-MTAB-7093:Au-COOH_20 nanometer_15ug/mL_r3

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-COOH_20 nanometer_15ug/mL_r3


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-7093:Au-COOH_20 nanometer_4ug/mL_r1a

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-COOH_20 nanometer_4ug/mL_r1a


text: public

text: E-MTAB-7093:Au-COOH_20 nanometer_4ug/mL_r2a

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-COOH_20 nanometer_4ug/mL_r2a


text: public

text: E-MTAB-7093:Au-COOH_20 nanometer_4ug/mL_r2b

text: ArrayExpress

text: monocyte

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-COOH_20 nanometer_4ug/mL_r2b


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-7093:Au-COOH_20 nanometer_4ug/mL_r3a

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: Au-COOH_20 nanometer_4ug/mL_r3a


characteristic: External Id

text: public

text: E-MTAB-7093:Au-COOH_5 nanometer_15ug/mL_r1

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-COOH_5 nanometer_15ug/mL_r1

characteristic: title


characteristic: INSDC center name

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characteristic: INSDC last update

text: public

text: E-MTAB-7093:Au-COOH_5 nanometer_15ug/mL_r2

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-COOH_5 nanometer_15ug/mL_r2


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

text: E-MTAB-7093:Au-COOH_5 nanometer_15ug/mL_r3

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-COOH_5 nanometer_15ug/mL_r3


text: public

characteristic: SRA accession

text: E-MTAB-7093:Au-COOH_5 nanometer_27ug/mL_r2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-COOH_5 nanometer_27ug/mL_r2


text: public

text: E-MTAB-7093:Au-COOH_5 nanometer_27ug/mL_r3

text: ArrayExpress

characteristic: cell line

text: monocyte

characteristic: cell type

text: human

characteristic: common name

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-COOH_5 nanometer_27ug/mL_r3


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-7093:Au-NR3_20 nanometer_15ug/mL_r1

text: ArrayExpress

text: monocyte

text: human

characteristic: description

text: acute monocytic leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-NR3_20 nanometer_15ug/mL_r1


characteristic: External Id

text: public

text: E-MTAB-7093:Au-NR3_20 nanometer_15ug/mL_r2

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: Au-NR3_20 nanometer_15ug/mL_r2


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7093:Au-NR3_20 nanometer_15ug/mL_r3

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-NR3_20 nanometer_15ug/mL_r3

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

text: E-MTAB-7093:Au-NR3_20 nanometer_4ug/mL_r1

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-NR3_20 nanometer_4ug/mL_r1


text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7093:Au-NR3_20 nanometer_4ug/mL_r2b

characteristic: Submitter Id

text: ArrayExpress

text: monocyte

text: human

text: Protocols: The undifferentiated monocytic THP.1 cell line was purchased from ATCC® (#TIB202). The cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 100 U/mL penicillin, 100 μg/mL streptomycin, and 0.05 mM β-mercaptoethanol. The cell density was strictly kept between 0.1 to 2 million cells/mL. Undifferentiated THP.1 cells (1 milion cells per condition) were exposed to the 6 Au NPs (two diameters 5 and 20 nm, and three functional surface groups -NR3+, -COOH and -PEG) at different doses for 6 h followed by RNA extraction. Based on the preliminary cytotoxicity screening we have determined the doses inducing 10% of cell death for Au-5-NH2 (EC10= 27 µg/mL) and Au-20-NH2 (EC10= 4 µg/mL). The EC10 values for the 4 other NPs were not determined (EC10> 100 µg/mL). In this pilot study, cells were exposed: (1) to the three Au-5(-NH2/-COOH/-PEG) NPs at a concentration of 27 µg/mL (corresponding to the individual EC10 dose for the set of 5 nm size NPs), (2) to the three Au-20(-NH2/-COOH/-PEG) NPs at a concentration of 4 µg/mL (corresponding to the individual EC10 dose for the set of 20 nm size NPs) or (3) to all the Au-5 and Au-20 (-NH2/-COOH/-PEG) at a concentration of 15 µg/mL (corresponding to the average EC10 dose). The control used was cells incubated with culture media only. Each condition was performed in triplicate. After exposure, the cells were washed twice with ice-cold PBS by centrifugation 300 g, 5 min at 4°C. The cells were lysed with 350 µL of Buffer RLT Plus, supplemented with β-mercaptoethanol, from the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). Samples were stored at -80°C before RNA/DNA extraction. Qiagen protocol was strictly applied. At the end of the procedure, RNA was eluted at once with 30 µL of RNAse free water. Aliquots of 3 µL of each RNA samples were prepared for quality analysis. The concentrations of total RNA were measured with Nanodrop spectrophotometer and Qbit fluorescence. The RNA samples were carefully labelled and stored at -80°C prior to sequencing. Bulk-RNA transcriptome analysis was performed by the STRT RNA-seq method (PMID: 22481528) with minor modifications (PMID: 26874359). Briefly, ten nanogram of high-quality input RNA was converted to cDNA and amplified to form an Illumina-compatible 46-plex library. ERCC RNA Spike-In Mix 1 (cat. 4456740; ThermoScientific) was used in 1000X dilution. In total, 25 PCR cycles were used, but as six base-pair unique molecular identifiers (UMIs) were applied, only the absolute number of unique reads was calculated per analyzed sample.

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-NR3_20 nanometer_4ug/mL_r2b


text: Division of Chemical Biology, Department of Biology and Biological Engineering

text: public

text: E-MTAB-7093:Au-NR3_20 nanometer_4ug/mL_r3a

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: monocyte

characteristic: cell type

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-NR3_20 nanometer_4ug/mL_r3a


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-7093:Au-NR3_20 nanometer_4ug/mL_r3b

text: ArrayExpress

text: monocyte

text: human

characteristic: common name

characteristic: description

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-NR3_20 nanometer_4ug/mL_r3b


characteristic: External Id

text: public

text: E-MTAB-7093:Au-NR3_5 nanometer_15ug/mL_r2

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-NR3_5 nanometer_15ug/mL_r2


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7093:Au-NR3_5 nanometer_15ug/mL_r3

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: Au-NR3_5 nanometer_15ug/mL_r3


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-7093:Au-NR3_5 nanometer_27ug/mL_r1

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-NR3_5 nanometer_27ug/mL_r1

characteristic: title


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7093:Au-NR3_5 nanometer_27ug/mL_r2

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-NR3_5 nanometer_27ug/mL_r2


text: public

text: E-MTAB-7093:Au-NR3_5 nanometer_27ug/mL_r3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-NR3_5 nanometer_27ug/mL_r3


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-7093:Au-PEG_20 nanometer_15ug/mL_r1

text: ArrayExpress

text: monocyte

characteristic: cell type

text: human

characteristic: common name

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-PEG_20 nanometer_15ug/mL_r1


characteristic: External Id

text: public

text: E-MTAB-7093:Au-PEG_20 nanometer_15ug/mL_r2

text: ArrayExpress

text: monocyte

text: human

characteristic: description

text: acute monocytic leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-PEG_20 nanometer_15ug/mL_r2


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7093:Au-PEG_20 nanometer_15ug/mL_r3

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-PEG_20 nanometer_15ug/mL_r3


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-7093:Au-PEG_20 nanometer_4ug/mL_r1b

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: Au-PEG_20 nanometer_4ug/mL_r1b


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-7093:Au-PEG_20 nanometer_4ug/mL_r2a

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-PEG_20 nanometer_4ug/mL_r2a

characteristic: title


text: public

characteristic: SRA accession

text: E-MTAB-7093:Au-PEG_20 nanometer_4ug/mL_r3a

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-PEG_20 nanometer_4ug/mL_r3a


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-7093:Au-PEG_5 nanometer_15ug/mL_r1

text: ArrayExpress

characteristic: cell line

text: monocyte

characteristic: cell type

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-PEG_5 nanometer_15ug/mL_r1


characteristic: External Id

text: public

text: E-MTAB-7093:Au-PEG_5 nanometer_15ug/mL_r2

text: ArrayExpress

text: monocyte

text: human

characteristic: common name

characteristic: description

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-PEG_5 nanometer_15ug/mL_r2


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7093:Au-PEG_5 nanometer_15ug/mL_r3

text: ArrayExpress

text: monocyte

text: human

text: Protocols: The undifferentiated monocytic THP.1 cell line was purchased from ATCC® (#TIB202). The cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 100 U/mL penicillin, 100 μg/mL streptomycin, and 0.05 mM β-mercaptoethanol. The cell density was strictly kept between 0.1 to 2 million cells/mL. Undifferentiated THP.1 cells (1 milion cells per condition) were exposed to the 6 Au NPs (two diameters 5 and 20 nm, and three functional surface groups -NR3+, -COOH and -PEG) at different doses for 6 h followed by RNA extraction. Based on the preliminary cytotoxicity screening we have determined the doses inducing 10% of cell death for Au-5-NH2 (EC10= 27 µg/mL) and Au-20-NH2 (EC10= 4 µg/mL). The EC10 values for the 4 other NPs were not determined (EC10> 100 µg/mL). In this pilot study, cells were exposed: (1) to the three Au-5(-NH2/-COOH/-PEG) NPs at a concentration of 27 µg/mL (corresponding to the individual EC10 dose for the set of 5 nm size NPs), (2) to the three Au-20(-NH2/-COOH/-PEG) NPs at a concentration of 4 µg/mL (corresponding to the individual EC10 dose for the set of 20 nm size NPs) or (3) to all the Au-5 and Au-20 (-NH2/-COOH/-PEG) at a concentration of 15 µg/mL (corresponding to the average EC10 dose). The control used was cells incubated with culture media only. Each condition was performed in triplicate. After exposure, the cells were washed twice with ice-cold PBS by centrifugation 300 g, 5 min at 4°C. The cells were lysed with 350 µL of Buffer RLT Plus, supplemented with β-mercaptoethanol, from the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). Samples were stored at -80°C before RNA/DNA extraction. Qiagen protocol was strictly applied. At the end of the procedure, RNA was eluted at once with 30 µL of RNAse free water. Aliquots of 3 µL of each RNA samples were prepared for quality analysis. The concentrations of total RNA were measured with Nanodrop spectrophotometer and Qbit fluorescence. The RNA samples were carefully labelled and stored at -80°C prior to sequencing. Bulk-RNA transcriptome analysis was performed by the STRT RNA-seq method (PMID: 22481528) with minor modifications (PMID: 26874359). Briefly, ten nanogram of high-quality input RNA was converted to cDNA and amplified to form an Illumina-compatible 46-plex library. ERCC RNA Spike-In Mix 1 (cat. 4456740; ThermoScientific) was used in 1000X dilution. In total, 25 PCR cycles were used, but as six base-pair unique molecular identifiers (UMIs) were applied, only the absolute number of unique reads was calculated per analyzed sample.

text: acute monocytic leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-PEG_5 nanometer_15ug/mL_r3


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Division of Chemical Biology, Department of Biology and Biological Engineering

text: public

text: E-MTAB-7093:Au-PEG_5 nanometer_27ug/mL_r1

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: Au-PEG_5 nanometer_27ug/mL_r1


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-7093:Au-PEG_5 nanometer_27ug/mL_r2

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: Au-PEG_5 nanometer_27ug/mL_r2


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: monocyte

text: human

text: acute monocytic leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

characteristic: title


E-MTAB-7107:nascentRNA 0h

characteristic: ENA-LAST-UPDATE

text: FAU Erlangen-Nurnberg Dept. Genetics

text: public

text: E-MTAB-7107:nascentRNA 0h

tag: Namespace:FAU Erlangen-Nurnberg Dept. Genetics

text: 3 to 6

unit: month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: hematopoietic multipotent progenitor cell

text: house mouse

text: Protocols: Primary hematopoietic precursor cells from C57/BL6 age 3 to 6 months old female mice were transformed in vitro by an tamoxifen inducible version of Hoxa9 (Hoxa9-ER). Samples were generated in the presence of active Hoxa9 (0h) and in a time series after Hoxa9 was inactivated by tamoxifen withdrawal at 8h, 16h, 24h, 48h, and 72h. nascent RNA isolation, cells were labeled with 4-thio-uridine for 1h before total RNA was extracted by standard methods. Labeled RNA was specifically biotinylated and separated by streptavidin chromatography. Selected RNA was recovered by cleavage of biotion crosslinkers and subjected to standard library construction methods. Illumina standard RNA library construction kit using Illumina TrueSeq RNA Library Preparation Kit

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

text: tamoxifen-inducible overexpression of Hoxa9

characteristic: phenotype

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: nascentRNA 0h


E-MTAB-7107:nascentRNA 16h

characteristic: External Id

text: FAU Erlangen-Nurnberg Dept. Genetics

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7107:nascentRNA 16h

text: 3 to 6

text: ArrayExpress

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus

text: female

text: nascentRNA 16h


E-MTAB-7107:nascentRNA 24h

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: FAU Erlangen-Nurnberg Dept. Genetics

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-7107:nascentRNA 24h

text: 3 to 6

text: ArrayExpress

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

characteristic: organism part

text: Mus musculus

text: female

text: nascentRNA 24h


E-MTAB-7107:nascentRNA 48h

characteristic: ENA-LAST-UPDATE

text: FAU Erlangen-Nurnberg Dept. Genetics

text: public

characteristic: SRA accession

text: E-MTAB-7107:nascentRNA 48h

characteristic: Submitter Id

text: 3 to 6

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus

text: female

text: nascentRNA 48h

characteristic: title


E-MTAB-7107:nascentRNA 72h

characteristic: External Id

text: FAU Erlangen-Nurnberg Dept. Genetics

characteristic: INSDC center name

text: public

text: E-MTAB-7107:nascentRNA 72h

text: 3 to 6

text: ArrayExpress

text: house mouse

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: phenotype

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: nascentRNA 72h


E-MTAB-7107:nascentRNA 8h

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: FAU Erlangen-Nurnberg Dept. Genetics

characteristic: INSDC first public

text: public

text: E-MTAB-7107:nascentRNA 8h

text: 3 to 6

text: ArrayExpress

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus

text: female

text: nascentRNA 8h


characteristic: ENA-LAST-UPDATE

text: GSC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: clone

text: Musa ABB Group

characteristic: organism

text: Musa ABB Group


characteristic: External Id

text: GSC

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: Musa AB Group

text: Musa AB Group


text: Wellcome Sanger Institute

text: public

tag: Namespace:Wellcome Sanger Institute

text: 6 to 12

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: T-helper 2 cell

text: house mouse

text: Protocols: Th2 cells were extracted from mouse spleen using Miltenyii naive CD4 T cell purification kit. Cells were treated with 15μM 4μ8c for 4 days Cells were activated on CD3/CD28 coated plated in IMDM + BME + IL4. Cells were transduced with retrovirus, either empty or with XBP1s (spliced form) overexpression. The day after some of the cells were additionally treated with 4u8c. Cells were harvested on day 5 for RNA-seq 5000 cells were sorted into 20ul RLT lysis buffer and purified with SPRI beads 1:1 cDNA was made and amplified using an adapted smartseq-2 protocol. Libraries were made using Nextera XT DNA Library Prep Kit

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: spleen

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

characteristic: INSDC first public

text: public

text: 6 to 12

text: ArrayExpress

text: T-helper 2 cell

characteristic: cell type

text: house mouse

characteristic: common name

text: XBP1s overexpression

text: Mus musculus

text: Mus musculus

text: spleen

text: Mus musculus

text: male

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Natural Resources Institute Finland (Luke)

text: cattle

text: Finland

characteristic: geographic location (country and/or sea)

text: Lapland

characteristic: geographic location (region and locality)

text: Bos taurus

text: Bos taurus

text: female

text: Whole blood RNA-Seq of North-Eurasian cattle


characteristic: External Id

text: Natural Resources Institute Finland (Luke)

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: cattle

text: Finland

text: Lapland

text: Bos taurus

characteristic: organism

text: Bos taurus

text: female


text: public

text: cattle

text: Russia

text: Yakutsk

text: Bos taurus

text: Bos taurus

text: female

characteristic: sex

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: WUR

text: public

characteristic: collection date

text: human

text: Neonatal faeces

characteristic: description

text: Faeces

characteristic: environment (biome)

text: Faeces

characteristic: environment (feature)

text: Faeces

characteristic: environment (material)

text: Netherlands

text: 52.5168° N

characteristic: geographic location (latitude)

text: 6.0830° E

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: mimarks-survey

characteristic: investigation type

text: Homo sapiens

characteristic: project name

text: Homo sapiens

text: MiSeq

characteristic: sequencing method

text: Neonatal faeces


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MAX F. PERUTZ LABORATORIES

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:MAX F. PERUTZ LABORATORIES

characteristic: Submitter Id

text: potato

characteristic: common name

text: NBS fragments isolated by amplification of potato cultivar MFII using R2-gene-specific primers (library prep 1). Sample donated by AIT, AT (obtained from CIP; PE)

text: Solanum tuberosum

text: Solanum tuberosum

text: NBS domains for cultivar MFII (library prep 1, miseq)


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MAX F. PERUTZ LABORATORIES

text: public

text: potato

text: NBS fragments isolated by amplification of potato cultivar MFII using R2-gene-specific primers (library prep 2). Sample donated by AIT, AT (obtained from CIP; PE)

characteristic: description

text: Solanum tuberosum

characteristic: organism

text: Solanum tuberosum

text: NBS domains for cultivar MFII (library prep 2, miseq)

characteristic: title


text: MAX F. PERUTZ LABORATORIES

text: public

text: potato

text: NBS fragments isolated by amplification of potato cultivar TPS67 using R2-gene-specific primers. Sample donated by AIT, AT (obtained from CIP; PE)

text: Solanum tuberosum

text: Solanum tuberosum

text: NBS domains for cultivar TPS67 (miseq)


text: MAX F. PERUTZ LABORATORIES

text: public

text: potato

text: NBS fragments isolated by amplification of potato cultivar MT_pool_M using R2-gene-specific primers. Sample donated by AIT, AT

text: Solanum tuberosum

text: Solanum tuberosum

text: NBS domains for cultivar MT_pool_M (miseq)


text: MAX F. PERUTZ LABORATORIES

text: public

text: potato

text: NBS fragments isolated by amplification of potato cultivar MT_pool_T using R2-gene-specific primers. Sample donated by AIT, AT

text: Solanum tuberosum

text: Solanum tuberosum

text: NBS domains for cultivar MT_pool_T (miseq)


text: MAX F. PERUTZ LABORATORIES

text: public

text: potato

text: NBS fragments isolated by amplification of potato cultivar MT_pool_S using R2-gene-specific primers. Sample donated by AIT, AT

text: Solanum tuberosum

text: Solanum tuberosum

text: NBS domains for cultivar MT_pool_S (miseq)


text: MAX F. PERUTZ LABORATORIES

text: public

text: potato

text: NBS fragments isolated by amplification of potato cultivar R2 using R2-gene-specific primers. Sample donated by AIT, AT (obtained from IPK at Groß Lüsewitz; DE)

text: Solanum tuberosum

text: Solanum tuberosum

text: NBS domains for cultivar R2 (miseq)


text: ANSES

text: public

characteristic: collection date

text: France

characteristic: geographic location (country and/or sea)

characteristic: isolate

text: sea food

characteristic: isolation source

text: Listeria monocytogenes

text: Listeria monocytogenes


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ANSES

text: public

text: France

text: Meat products

text: Listeria monocytogenes

text: Listeria monocytogenes


text: ANSES

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: France

text: Industrial environnement

text: Listeria monocytogenes

text: Listeria monocytogenes


characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:UNIVERSITY OF SHEFFIELD, DEPARTMENT OF ANIMAL & PL

text: Basalt sample 1

characteristic: environment (biome)

characteristic: environment (feature)

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: rock metagenome

text: Basalt associated fungal communities

characteristic: project name

text: rock metagenome

text: MiSeq

characteristic: sequencing method

text: Basalt associated fungal communities


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF SHEFFIELD, DEPARTMENT OF ANIMAL & PL

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Basalt sample 2

characteristic: description

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: metagenome

text: rock metagenome

characteristic: organism

text: Basalt associated fungal communities

text: rock metagenome

text: MiSeq

text: Basalt associated fungal communities

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:CENTER FOR BIOTECHNOLOGY, BIELEFELD UNIVERSITY

text: ‘Börner’ (Vitis riparia x Vitis cinerea)

text: Vitis riparia x Vitis cinerea

text: Vitis riparia x Vitis cinerea

text: young leaf

characteristic: tissue lib

text: Boerner