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TranscriptomicsiRNA-seq: Computational method for genome wide assessment of acute transcriptional regulation from total RNA-seq data
RNA-seq is a sensitive and accurate technique to compare steady state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se, other technologies are needed to more precisely determine acute transcriptional responses. Here, we ha...
ORGANISM(S): Homo sapiens 
2015-02-04 | E-GEOD-60462 | biostudies-arrayexpress
ProteomicsA. muciniphila, B. longum, E. coli, headspace metabolites
Culture headspaces of A. muciniphila, B. longum, E. coli, and sterile media controls using sorbent tubes and GCMS (Figure 3C)
ORGANISM(S): Bifidobacterium Longum Subsp. Longum (ncbitaxon:1679) Escherichia Coli (ncbitaxon:562) Bhi-mucin Akkermansia Muciniphila (ncbitaxon:239935) 
2024-07-15 | MSV000095341 | MassIVE
ProteomicsBreath Metabolites from Healthy and Asthmatic Children
mzML files used to generate Figure 1 A-F, Figure S1 D-E, Figure 6 B, Figure S5 D-F. Breath samples collected from healthy and asthmatic children
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-07-15 | MSV000095340 | MassIVE
ProteomicsThe exhaled breath of humanized mice
This is GCxGC MS data from exhaled breath from humanized mice as well as germ-free controls. Raw files in CDF format (Figure S4D-F of associated publication)
ORGANISM(S): C57bl/6 Mice 
2025-08-15 | MSV000098837 | MassIVE
ProteomicsMetabolites from anaerobic culture headspace
This is GCxGC MS data from headspace VOCs from A. muciniphila, B. thetaiotaomicron, Collinsella aerofaciens, E. coli, and Ruminococcus torques and sterile media controls. Raw files in CDF format. (Fig 4A , Fig 5, Fig 3B from associated publication)
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Bacteroides Thetaiotaomicron (ncbitaxon:818) Collinsella Aerofaciens (ncbitaxon:74426) Akkermansia Muciniphila (ncbitaxon:239935) [ruminococcus] Torques (ncbitaxon:33039) 
2025-07-30 | MSV000098693 | MassIVE
ProteomicsThe exhaled breath of monocolonized mice
This is GCxGC MS raw data from exhaled breath from colonized gnotobiotic mice with one of five common gut commensals including A. muciniphila, B. thetaiotaomicron, Collinsella aerofaciens, E. coli, and Ruminococcus torques and sterile media controls. Raw files in CDF format. (Fig 4B, Fig 5 from asso...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Gnotobiotic Mice Bacteroides Thetaiotaomicron (ncbitaxon:818) Collinsella Aerofaciens (ncbitaxon:74426) Akkermansia Muciniphila (ncbitaxon:239935) [ruminococcus] Torques (ncbitaxon:33039) 
2025-07-30 | MSV000098692 | MassIVE
ProteomicsExhaled breath from conventional and conventionalized mice
This is GCxGC MS data from exhaled breath from conventional and conventionalized mice as well as germ-free controls. Raw files in CDF format (Figure 2A-F, Figure S3A-B from our publication)
ORGANISM(S): Gnotobiotic Mice 
2025-07-30 | MSV000098688 | MassIVE
ProteomicsExamples of output air collected from a mice ventilator
Examples of output air collected from a mice ventilator. mzML files used to generate Figure 6S C.
ORGANISM(S): C57bl/6 Mice 
2025-07-30 | MSV000098687 | MassIVE
ProteomicsExhaled breath of mice receiving daily isoprene doses
mzML files used to generate Figure 6S B. Isoprene in the exhaled breath of mice receiving daily isoprene doses for 14 days, and exhaled breath of mice receiving concurrent daily vehicle controls, or in the ambient air alone
ORGANISM(S): C57bl/6 Mice 
2025-07-30 | MSV000098686 | MassIVE
GenomicsAcute TNF-induced repression of cell identity genes is mediated by NFkB-directed redistribution of cofactors from super-enhancers
The proinflammatory cytokine tumor necrosis factor (TNF) plays a central role in low-grade adipose tissue inflammation and development of insulin resistance during obesity. In this context, nuclear factor kappa-light-chain-enhancer of activated B cells (NFkB), is directly involved and required for t...
ORGANISM(S): Homo sapiens 
2015-06-17 | E-GEOD-64233 | biostudies-arrayexpress
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