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GenomicsThe long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites
Long noncoding RNAs (lncRNAs) are important regulators of chromatin; however, the mechanistic roles for many lncRNAs are poorly understood in part because their direct interactions with genomic loci and proteins are difficult to assess. We used CHART-seq to map the genomic binding sites for two high...
ORGANISM(S): Homo sapiens 
2014-08-12 | E-GEOD-58444 | biostudies-arrayexpress
TranscriptomicsGene expression profile of calcified and normal tricuspid aortic valves by RNA sequencing.
Purpose: Calcific aortic valve stenosis (AS) is a fatal disease with currently no medical therapy. Some genes were associated with AS, but the genetic architecture of the disease has yet to be discovered. The objective of this study was to combine genome-wide association studies (GWAS) and gene expr...
ORGANISM(S): Homo sapiens 
2015-12-09 | E-GEOD-55492 | biostudies-arrayexpress
TranscriptomicsscRNA-seq analysis of enriched CD4+ T cells from lung tissues after single or combined AIT treatment strategies with AhR agonist 10-Cl-BBQ in a murine model of OVA-induced allergic airway inflammation (AAI)
Allergen-specific immunotherapy (AIT) is able to restore immune tolerance to allergens in allergic patients. However, some patients do not or only poorly respond to current treatment protocols. Therefore, there is a need for deeper mechanistic insights and further improvement of treatment strategies...
ORGANISM(S): Mus musculus 
2024-05-06 | E-MTAB-14030 | biostudies-arrayexpress
TranscriptomicsUSR_template_replicates
Next-generation sequencing (NGS) of antibody variable regions has emerged as a powerful tool in systems immunology by providing quantitative molecular information on polyclonal humoral immune responses. Reproducible and robust information on antibody repertoires is valuable for basic and applied imm...
ORGANISM(S): Mus musculus 
2013-10-26 | E-MTAB-1896 | biostudies-arrayexpress
TranscriptomicsGene Expression in Mutant P0 Cre Dicer Mouse Sciatic Nerves
The hypothesis is that genes involved in the immature schwann cell and promyelinating state will be upregulated and genes that are involved in the myelnating state will be down regulated. Bioconductor limma package [1,2,3,4] was used to preprocess 6 samples from mouse tissue-cultured cells, which ...
ORGANISM(S): Mus musculus 
2010-06-16 | E-GEOD-16741 | biostudies-arrayexpress
TranscriptomicsCharacterisation of LAP/LIP transcriptional signature in human hepatoma cells
BACKGROUND & AIMS: C/EBPbeta is involved in numerous process as carcinogenesis but its role is still not clear due to the existence of an active form (LAP) and an inhibitory form (LIP) of this transcription factor. The main goals of the present research were (i) the identification of genes inversely...
ORGANISM(S): Homo sapiens 
2010-05-22 | E-GEOD-15010 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of rat severed medial collateral ligament following injury
Gene Expression Profiling of Severed Rat Medial Collateral Ligament at 1, 2, 4, 7,1 0, and 14 days Following Injury with Control and Cultured Ligament Fibroblasts and Rat Universal Reference RNA; The aim of this study was to assess the genes involved in the repair of the the dense connective tissue ...
ORGANISM(S): Rattus norvegicus 
2008-04-05 | E-GEOD-10720 | biostudies-arrayexpress
TranscriptomicsNeutrophil-derived IL-1β is sufficient for abscess formation in immunity against Staphylococcus aureus in mice
Neutrophil abscess formation is critical in innate immunity against many pathogens. Here, the mechanism of neutrophil abscess formation was investigated using a mouse model of Staphylococcus aureus cutaneous infection. Gene expression analysis of S. aureus-infected skin revealed that induction of ne...
ORGANISM(S): Mus musculus 
2012-12-05 | E-GEOD-36826 | biostudies-arrayexpress
TranscriptomicsTranscriptome analysis of ATRX and DAXX knockout mouse ESC
PolyA+ RNA-Seq was performed on wildtype, ATRX and DAXX knockout cells derived by CRISPR targeting (Sadic et. al, EMBO Rep, 16(7), p836-850, 2015, DOI: 10.15252/embr.201439937). PolyA+ RNA-Seq was performed on wildtype, ATRX and DAXX knockout cells derived by CRISPR targeting (Sadic et. al, EMBO Rep...
ORGANISM(S): Mus musculus 
2015-10-26 | E-GEOD-73881 | biostudies-arrayexpress
TranscriptomicsMethod Study
High-throughput sequencing (HTS) of antibody amplicon libraries has become a powerful method in the emerging field of systems immunology. However, numerous sources of bias in HTS workflows may affect antibody repertoire data. A crucial step in antibody amplicon library preparation is the addition of...
ORGANISM(S): Mus musculus 
2014-02-20 | E-MTAB-2226 | biostudies-arrayexpress
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