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GenomicsGenome-wide mapping of OCT4, NANOG and CTCF in human embryonic stem cells
Transcription factors and their specific interactions with targets are crucial in specifying gene expression programs. To gain insights into the transcriptional regulatory networks in embryonic stem cells, we used chromatin immunoprecipitation coupled to ultra-high-throughput DNA sequencing (ChIP-se...
ORGANISM(S): Homo sapiens 
2010-03-06 | E-GEOD-20650 | biostudies-arrayexpress
TranscriptomicsThe effect of HO-1 overexpression on microRNA transcriptome in NCI-H292 lung cancer cells
The aim was to determine the effect of heme oxygenase-1 (HO-1) overexpression on microRNA transcriptome in human non-small cell lung carcinoma cell line (NCI-H292). Since the cells of different HO-1 genotypes were used (cells are after retroviral transduction with empty vector with normal level of H...
ORGANISM(S): Homo sapiens 
2013-04-27 | E-GEOD-37779 | biostudies-arrayexpress
ProteomicsThe domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)
A large fraction of plant genomes is composed of transposable elements (TE), which provide a potential source of novel genes through “domestication” – the process whereby the proteins encoded by TE diverge in sequence, lose their ability to catalyse transposition and instead acquire novel functions ...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2020-05-18 | PXD018911 | Pride
Polycomb repressive complex 2 Alp1 Arabidospsis thaliana Harbinger transposable elements Alp2 
TranscriptomicsTranscriptional profiling of Salmonella typhimurium in the ceca of gnotobiotic mice
Transcriptional profiling of Salmonella typhimurium in the ceca of germ-free and Bacteroides thetaiotaomicron-monoassociated gnotobiotic mice. Comparison with response in MM-Glucose. In vivo transcriptional profiles of Salmonella typhimurium obtained from biological triplicate samples taken from cec...
ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 
2013-07-23 | E-GEOD-49076 | biostudies-arrayexpress
TranscriptomicsSingle-cell RNAseq of PBMC from mice infected with Dengue virus
Single-cell RNAseq of PBMC from mice infected with either WT DENV2 or a T209 mutant DENV2
ORGANISM(S): Mus musculus 
2026-04-21 | E-MTAB-15296 | biostudies-arrayexpress
TranscriptomicsSex differences in the translatome of Drosophila fruitless-expressing neurons that underlie reproductive behaviors
Adult reproductive behaviors in Drosophila melanogaster males and females are vastly different. Yet, neurons that express sex-specifically spliced fruitless transcripts (fru P1) underlie these behaviors in both sexes. How the same set of neurons can drive such different behaviors is an important an...
ORGANISM(S): Drosophila melanogaster 
2015-09-01 | E-GEOD-67743 | biostudies-arrayexpress
ProteomicsDose and route of administration determine the efficacy of prophylactic immunotherapy for peanut allergy in a Brown Norway rat model
MS/MS analysis of the peanut protein extract (PPE) confirmed the presence of the four major peanut allergens and identified the presence of Ara h 1 isotypes, Ara h 2 isotypes, Ara h 3 isotypes, Ara h 6 isotypes and Ara h 7 isotypes. Allergen-specific immunotherapy (IT) is emerging as a viable option...
ORGANISM(S): Arachis hypogaea (Peanut) 
2023-02-21 | PXD039324 | Pride
Food allergy Arachis hypogaea Mass spectrometry Peanut 
TranscriptomicsExpression data from untreated vs. BMP4-treated cultured wild-type and MuSK null muscle cells (myoblasts and myotubes)
Bone morphogenic proteins (BMPs) function in virtually all tissues with cell-type specific outcomes. Since there are a relatively small number of BMP receptors this exquisite signaling specificity requires additional molecules to regulate the output of this pathway. We demonstrated that the recepto...
ORGANISM(S): Mus musculus 
2015-08-03 | E-GEOD-59567 | biostudies-arrayexpress
TranscriptomicsRNA-seq experiment in J20 hAPP mice and littermate controls measuring total RNA in lysate of microdissected dentate gyrus
∆FosB epigenetically regulates target gene expression; however, whether ∆FosB targets the same genes when induced by recurrent seizures in different neurological conditions like Alzheimer's disease (AD) is unclear. We performed hippocampal ChIP-sequencing to identify ∆FosB target genes in APP mice, ...
ORGANISM(S): Mus musculus 
2020-04-16 | E-MTAB-8963 | biostudies-arrayexpress
TranscriptomicsComparison of systematic sequencing errors using spike-in standards
While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants. These SSEs can cause base quality scores to underestimate the proba...
ORGANISM(S): Homo sapiens 
2012-03-03 | E-GEOD-36217 | biostudies-arrayexpress
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