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MetabolomicsComposition of the marine exometabolome is more stable than the functionally redundant microbial community in the oligotrophic North Atlantic

Untargeted features from the Bermuda Atlantic Time-series Study (BATS) site collected during the time period spanning 2016 to 2019. Metabolites were sampled from surface seawater to 1000 m deep and throughout the year. Dissolved organic matter extracts were analyzed in positive and negative ion m...

2024-02-28 | MTBLS5228 | MetaboLights
TranscriptomicsTranscriptomic responses of Atlantic salmon (Salmo salar) to environmental enrichment during juvenile rearing
Captive rearing programs (hatcheries) are often used in conservation and management efforts for at-risk salmonid fish populations. However, hatcheries typically rear juveniles in environments that contrast starkly with natural conditions, which may lead to phenotypic and/or genetic changes that adve...
ORGANISM(S): Salmo salar 
2014-12-10 | E-GEOD-63982 | biostudies-arrayexpress
TranscriptomicsCircularized chromosome conformation capture (4C-seq) in A549 cells after glucocorticoid re-induction
We performed 4C-seq in the A549 cell line to investigate changes in chromatin interactions at the ZBTB16 locus. Cells were treated with either 100 nM dexamethasone or 0.1% ethanol. After 4 hours, cells were washed 2x with PBS and cultured in hormone-free medium for 24 hours, after which cells were t...
ORGANISM(S): Homo sapiens 
2021-05-03 | E-MTAB-9915 | biostudies-arrayexpress
ProteomicsLC-MSMS analysis of Meloidogyne incognita feeding tube enriched samples isolated from tobacco and tomato giant cell cytoplasm
Here we developed a protocol for the isolation and semi-purification of root-knot nematode feeding tubes from giant-cell cytoplasm of several host plant species. Our methods allowed for the isolation and solubilization of sufficient quantities of enriched feeding tubes enabling a comparative proteom...
ORGANISM(S): Meloidogyne incognita Nicotiana tabacum (Common tobacco) Solanum lycopersicum 
2026-02-16 | PXD065741 | Pride
Tobacco Tomato Meloidogyne incognita Root-knot nematode Giant cell Feeding tube 
TranscriptomicsStudying enhancer activity by FAIRE-STARR-seq in the U2OS-GR and the U2OS-AR cells upon hormone treatment
To quantify functional enhancers, we performed STARR-seq (Self-Transcribing Active Regulatory Region sequencing) in the U2OS-GR and the U2OS-AR cell lines (derived from U2OS ATTC:HTB-96, stably transfected with an expression construct for rat GR or human AR, respectively). U2OS-GR cells were treated...
ORGANISM(S): Homo sapiens 
2021-03-09 | E-MTAB-9614 | biostudies-arrayexpress
MetabolomicsOrganotypic microfluidic breast cancer model reveals starvation-induced spatial-temporal metabolic adaptations
BACKGROUND: Ductal carcinoma in situ (DCIS) is the earliest stage of breast cancer. During DCIS, tumor cells remain inside the mammary duct, growing under a microenvironment characterized by hypoxia, nutrient starvation, and waste product accumulation; this harsh microenvironment promotes genomic in...
2019-02-08 | MTBLS669 | MetaboLights
ProteomicsFallopian tube secreted proteins affect ovarian metabolites in high grade serous ovarian cancer
Data files from Q Exactive were imported into Proteome Discoverer (version 2.2, Thermo Fisher) and analyzed using a label-free quantitation method. For MOE PTENshRNA protein IDs, MOE PTENshRNA results were compared to MOE SCRshRNA results against a Mus musculus database (10090_20160912 fasta file) a...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) 
2022-07-11 | MSV000089866 | MassIVE
ProteomicsProteomic changes following knockdown of DNA repair and redox signaling protein, APE1/Ref-1, under hypoxia conditions
Pancreatic cancer is a complex disease with a desmoplastic stroma, extreme hypoxia, and inherent resistance to therapy. Understanding the signaling and adaptive response of such an aggressive cancer is key to making advances in therapeutic efficacy and understanding disease progression. Redox factor...
ORGANISM(S): Homo sapiens (Human) 
2021-09-09 | PXD020515 | Pride
Transcription factor signaling Ape1/ref-1 Dna repair Pancreatic cancer Hypoxia 
GenomicsPacbio Hifi sequencing of a naked mole-rat male subordinate kidney sample
Two PacBio Hifi sequencing runs from the kidney of a single male NMR sample used to make the mHetGla4.1.primary genome assembly. Specifically, we assembled a second NMR genome from an unrelated male of a separate captive colony in Toronto, Canada, using PacBio HiFi (155.8 Gb, read N50 = 11.45 Kb) an...
ORGANISM(S): Heterocephalus glaber 
2026-08-05 | E-MTAB-17313 | biostudies-arrayexpress
GenomicsONT R10.4-Lsk sequencing of a naked mole-rat male subordinate. Sheared kidney, unsheared kidney, and brain samples
Two PacBio Hifi sequencing runs from the kidney of a single male NMR sample used to make the mHetGla4.1.primary genome assembly. Specifically, we assembled a second NMR genome from an unrelated male of a separate captive colony in Toronto, Canada, using PacBio HiFi (155.8 Gb, read N50 = 11.45 Kb) an...
ORGANISM(S): Heterocephalus glaber 
2026-08-06 | E-MTAB-17334 | biostudies-arrayexpress
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