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TranscriptomicsArchetypeShift: An R Package Integrating KEGG-Informed Pathway Analysis and IPA-Derived Functional Predictions for Validation of Single-Cell Archetypes
Archetype analysis is important because clustering of cell types is often nuanced and inexact. We developed a new pipeline to identify and annotate single-cell archetypes from preterm infant small intenstine organoids.
ORGANISM(S): Homo sapiens 
2026-06-30 | GSE334564 | GEO
TranscriptomicsReal time PCR from expression microdissection (xMD) of epithelial cells
The goal of this experiment was to determine the extent to which the xMD method can enrich for a specific cell type. Here we optimized each step of the xMD process from tissue retrieval, tissue transfer, film preparation, and RNA isolation to increase RNA yields and specficity. Duodenum (small inten...
ORGANISM(S): Homo sapiens 
2022-06-01 | GSE205216 | GEO
TranscriptomicsExpression data from human jejunum before and one month after Roux en Y Gastric Bypass (RYGB)
RYGB reconfigures the intenstine such that food enters the jejunum after passing only a small gastric pouch. This new anatomy places the jejunum as the first part of the intestine that interacts with the food, with little to no gastric digestion, causing dramatic changes in jejunal morphology. Basel...
ORGANISM(S): Homo sapiens 
2018-07-09 | GSE113819 | GEO
GenomicsArchetypeShift: An R Package Integrating KEGG-Informed Pathway Analysis and IPA-Derived Functional Predictions for Validation of Single-Cell Archetypes
ArchetypeShift: An R Package Integrating KEGG-Informed Pathway Analysis and IPA-Derived Functional Predictions for Validation of Single-Cell Archetypes
PRJNA1475458 | ENA
TranscriptomicsThe protein disulfide isomerase AGR2 is essential for the production of intestinal mucus
Protein disulfide isomerases (PDIs) aid protein folding and assembly by catalyzing formation and shuffling of cysteine disulfide bonds in the endoplasmic reticulum (ER). Many members of the PDI family are expressed in mammals but the roles of specific PDIs in vivo are poorly understood. A recent hom...
ORGANISM(S): Mus musculus 
2010-05-19 | E-GEOD-12503 | biostudies-arrayexpress
ProteomicsProfiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device
The spatiotemporal structure of the human microbiome, proteome, and metabolome reflects and determines regional intestinal physiology and may have implications for disease. Yet, we know little about the distribution of microbes, their environment, and their biochemical activity in the gut because of...
ORGANISM(S): Homo sapiens (Human) 
2023-01-18 | PXD038906 | Pride
Sampling device Human Gut Spatiotemporal Intenstine Microbiome 
GenomicsExpression data from human jejunum before and one month after Roux en Y Gastric Bypass (RYGB)
Expression data from human jejunum before and one month after Roux en Y Gastric Bypass (RYGB)
PRJNA454107 | ENA
GenomicsGene expression of donor monocytes recovered from various tissues of recipient mice one day after transfer
Gene expression of donor monocytes recovered from various tissues of recipient mice one day after transfer
PRJNA548331 | ENA
GenomicsReal time PCR from expression microdissection (xMD) of epithelial cells
Real time PCR from expression microdissection (xMD) of epithelial cells
PRJNA844103 | ENA
GenomicsExpression in donor monocyte derived cells
Expression in donor monocyte derived cells
PRJNA548315 | ENA
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