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GenomicsMapping mitochondrial DNA recombination in yeast
In this study, we present the first genome-wide recombination map for mitochondrial DNA in yeast. We also assess the impact of the genetic background and of several gene deletions on the recombination profiles.
ORGANISM(S): Saccharomyces cerevisiae 
2014-10-22 | E-MTAB-2474 | biostudies-arrayexpress
TranscriptomicsLinkage of Meis1 leukemogenic activity to multiple downstream effectors including Trib2 and Ccl3
OBJECTIVE: MEIS1, a HOX cofactor, collaborates with multiple HOX and NUP98-HOX fusion proteins to accelerate the onset of acute myeloid leukemia (AML) through largely unknown molecular mechanisms. MATERIALS AND METHODS: To further resolve these mechanisms, we conducted a structure-function analysis ...
ORGANISM(S): Mus musculus 
2009-04-09 | E-GEOD-15541 | biostudies-arrayexpress
ProteomicsDissecting Branch-Specific Unfolded Protein Response Activation in Drug-Tolerant BRAF-Mutant Melanoma using Data-Independent Acquisition
Cells rely on the Unfolded Protein Response (UPR) to maintain ER homeostasis (proteostasis) when faced with elevated levels of misfolded and aggregated proteins, which can hinder the secretion of properly folded proteins. The UPR is composed of three main branches—ATF6, IRE1, and PERK—that coordinat...
ORGANISM(S): Homo sapiens (Human) 
2025-08-25 | PXD061073 | Pride
Proteomics automation Activating transcription factor 6 Data-independent acquisition (dia) Inositol requiring enzyme 1 Protein kinase r-like er kinase Unfolded protein response 
TranscriptomicsDual RNA-seq – sRNA profiling in various cell types
Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal...
ORGANISM(S): mixed sample: human cell line CaCo-2 and Salmonella Typhimurium SL1344 
2015-12-11 | E-GEOD-67947 | biostudies-arrayexpress
TranscriptomicsGenome-wide study of nuclear poly(A) binding protein Nab2p depletion
Polyadenylation of mRNA is a key step in eu- karyotic gene expression. However, despite the ma- jor impact of poly(A) tails on mRNA metabolism, the precise roles of poly(A)-binding proteins (PABPs) in nuclear mRNA biogenesis remain elusive. Here, we demonstrate that rapid nuclear depletion of the S....
ORGANISM(S): Saccharomyces cerevisiae 
2015-08-13 | E-GEOD-65001 | biostudies-arrayexpress
TranscriptomicsDual RNA-seq of diverse human, mouse and pig cell-types infected with various Salmonella strains
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): mixed sample: human cell line AGS and Salmonella Typhimurium SL1344 
2015-12-11 | E-GEOD-60144 | biostudies-arrayexpress
TranscriptomicsChromatin accessibility in naive and primed HeLa cells upon IFNγ treatment
chromatin accessibility (ATAC-seq) experiment. HeLa cells were primed with IFNγ for 24 hours, followed by IFNγ washout. After 48h, naïve and primed cells were induced by IFNγ for 1h and 3h. Cells were harvested at indicated time points and processed for ATAC-seq.
ORGANISM(S): Homo sapiens 
2023-05-06 | E-MTAB-12624 | biostudies-arrayexpress
TranscriptomicsDual RNA-seq – Comparative RNA-seq (in vitro medium shift experiment)
Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal...
ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium 
2015-12-11 | E-GEOD-67949 | biostudies-arrayexpress
TranscriptomicsGain of chromatin loops marks the exit from naïve pluripotency – in-situ Hi-C data
In-situ Hi-C data for mouse embryonic stem cells (ES cells, grown in the presence of FBS and LIF) and for NS cells.
ORGANISM(S): Mus musculus 
2018-11-08 | E-MTAB-6591 | biostudies-arrayexpress
TranscriptomicsKC001: Genome wide expression profiling of the mesodiencephalic region led to the identification of novel factors involved in early and late dopaminergic development.
Meso-diencephalic dopaminergic (mdDA) neurons are critical for motor control and cognitive functioning and their loss or dysfunction is associated with disorders such as Parkinson’s disease (PD), schizophrenia and addiction. However, relatively little is known about the molecular mechanisms underlyi...
ORGANISM(S): Mus musculus 
2012-07-08 | E-GEOD-35326 | biostudies-arrayexpress
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