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MetabolomicsMetabolic Drug Response Phenotyping in Colorectal Cancer Organoids by LC-QTOF-MS
As metabolic rewiring is crucial for cancer cell proliferation, metabolic phenotyping of patient-derived organoids is desirable to identify drug-induced changes and trace metabolic vulnerabilities of tumor subtypes. We established a novel protocol for metabolomic and lipidomic profiling of colorecta...
2021-10-12 | MTBLS2130 | MetaboLights
TranscriptomicsChromatin immunoprecipitation of Foxp3 in mouse T-cell hybridoma cells
The forkhead transcription factor Foxp3 is essential for the development of CD4+CD25+ regulatory T (Treg) cells and prevention of autoimmunity, but how it controls the Treg gene expression program is not understood. We describe here genome-wide location and expression data that identify Foxp3 targe...
ORGANISM(S): Mus musculus 
2007-01-27 | E-TABM-154 | biostudies-arrayexpress
TranscriptomicsGenome-wide CpG methylation during osteogenic and myogenic differentiation from adipose- derived stem cells.
In the current study, we have performed a high-throughput CpG methylation analysis of well characterized and defined populations of human adipose-derived stem cells (hASCs) before and after in vitro induction of osteogenic and myogenic differentiation that allows identifying DNA methylation- regulat...
ORGANISM(S): Homo sapiens 
2014-01-02 | E-GEOD-33896 | biostudies-arrayexpress
GenomicsEpigenomic analysis of primary human T cells reveals novel enhancers associated with Th2 memory differentiation and asthma susceptibility (3 cell types)
A characteristic feature of asthma is the aberrant accumulation, differentiation or function of memory CD4+ T cells that produce Th2 cytokines (Th2 cells). By mapping genome-wide histone modification profiles of T cell subsets isolated from peripheral blood of healthy and asthmatic individuals, we i...
ORGANISM(S): Homo sapiens 
2014-07-05 | E-GEOD-53643 | biostudies-arrayexpress
TranscriptomicsTransposable element expression at unique loci in single cells with CELLO-seq
We introduce a novel method (CELLO-seq) for long-read RNA sequencing at single cell resolution. CELLO-seq allows for full-length RNA sequencing and enables measurement of allelic, isoform and Transposable Element (TE) expression at unique loci. We use CELLO-seq to assess the widespread expression of...
ORGANISM(S): Homo sapiens 
2020-10-01 | E-MTAB-9577 | biostudies-arrayexpress
TranscriptomicsChIP-chip from lymph node-derived primary lymphocytes with anti-E2F2 and anti-SV40TAg
E2F2 is essential for the maintenance of T lymphocyte quiescence. To identify the full set of E2F2 target genes, and to gain further understanding of the role of E2F2 in transcriptional regulation, we have performed ChIP-chip analyses across the genome of lymph node-derived T lymphocytes. Here we sh...
ORGANISM(S): Mus musculus 
2014-01-09 | E-GEOD-53888 | biostudies-arrayexpress
TranscriptomicsTranscriptome analysis of the Trypanosoma cruzi life-cycle
To generate a high quality, annotated gene expression database of T. cruzi trypomastigotes(TRP), amastigotes (AMA), epimastigotes (EPI), and metacyclic trypomastigotes (MET). The global assessment of transcript abundances in each life-cycle stage of T. cruzi will identify stage-regulated genes and p...
ORGANISM(S): Trypanosoma cruzi 
2010-05-15 | E-GEOD-14641 | biostudies-arrayexpress
TranscriptomicsPathway simulations in common oncogenic drivers of leukemic and rhabdomyosarcomatic cells: a systems biology approach
A part of current research has intensively been focused on the proliferation and metabolic processes governing biological systems. Since the advent of high throughput methodologies like microarrays, the load of genomic data has increased geometrically and along with that the need for computational m...
ORGANISM(S): Homo sapiens 
2011-12-20 | E-GEOD-34522 | biostudies-arrayexpress
GenomicsDNA-seq of differentially induced promoter regions in E. coli UTI89 strain grown in either J82 bladder epithelial cells, urine, DMEM or LB medium.
The method DFI-seq was developed to enable identification of differentially expressed genes in uropathogenic E. coli strain UTI89 during growth in human urine and in bladder epithelial cells. By utilising this new method, the aim was to identify novel virulence genes in UTI89. DFI-seq is a combinati...
ORGANISM(S): Escherichia coli UTI89 
2017-05-01 | E-MTAB-5657 | biostudies-arrayexpress
TranscriptomicsB-type lamins differentially associate with specific genes during differentiation without directly affecting their expression
B-type lamins, the major structural component of the nuclear lamina, is thought to play a repressive role in the expression of many of its bound genes whose silencing are known to be critical for cell differentiation during early development. Using global mapping of lamin-B-chromatin interaction, w...
ORGANISM(S): Mus musculus 
2011-10-31 | E-GEOD-24532 | biostudies-arrayexpress
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