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TranscriptomicsA search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation.
Analysis of the intergenic regions of Staphylococcus aureus by bioinformatics predicted multiple regulatory regions. From this analysis, we also characterized 11 novel noncoding RNAs (RsaA-K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumu...
ORGANISM(S): Staphylococcus aureus 
2010-05-18 | E-GEOD-17135 | biostudies-arrayexpress
Proteomics,MultiomicsProteomics of U1810 cells upon treatment with microRNAs with an AAGUGC seed motif.
microRNA dysregulation is a common feature of cancer cells, but the complex roles of microRNAs in cancer are not fully elucidated. Here we used functional genomics to identify oncogenic microRNAs in non-small cell lung cancer and to evaluate their impact on response to EGFR targeting therapy. Our da...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-31 | MSV000080829 | MassIVE
GenomicsZFP57 recognizes multiple and closely spaced sequence motif variants to maintain repressive epigenetic marks in mouse embryonic stem cells
In mouse embryonic stem cells SNPs disrupting closely-spaced hexanucleotide motifs are associated with lack of ZFP57 binding and H3K9me3 enrichment. Examination of ZFP57-KAP1 allele-specific binding in two lines of mouse embryonic stem cells JB1 and BJ1 generated from F1 hybrids derived from JF1 x B...
ORGANISM(S): Mus musculus 
2015-11-06 | E-GEOD-74757 | biostudies-arrayexpress
GenomicsEnhancers display sequence flexibility constrained by transcription factor motif syntax [Drosophila motif pasting STARR-seq]
Enhancers display sequence flexibility constrained by transcription factor motif syntax [Drosophila motif pasting STARR-seq]
PRJNA871262 | ENA
GenomicsEnhancers display sequence flexibility constrained by transcription factor motif syntax [Human motif pasting STARR-seq]
Enhancers display sequence flexibility constrained by transcription factor motif syntax [Human motif pasting STARR-seq]
PRJNA871264 | ENA
TranscriptomicsGlobal Analysis of Glucocorticoid Receptor-Associated Transcripts and Identification of a Target RNA Motif
Posttranscriptional regulation is emerging as a key factor in glucocorticoid (GC)-mediated gene regulation. We investigated the role of the human glucocorticoid receptor (GR) as an RNA-binding protein and its effect on mRNA turnover in human airway epithelial cells. Cell treatment with the potent ...
ORGANISM(S): Homo sapiens 
2011-06-24 | E-GEOD-24748 | biostudies-arrayexpress
GenomicsSomatic hypermutation patterns in immunoglobulin variable regions are dictated by a motif-specific sequence grammar and motif position
Somatic hypermutation patterns in immunoglobulin variable regions are dictated by a motif-specific sequence grammar and motif position
PRJNA1193086 | ENA
OtherEnhancers display sequence flexibility constrained by transcription factor motif syntax [Human motif pasting STARR-seq]
The information about when and where each gene is to be expressed is mainly encoded in the DNA sequence of enhancers, sequence elements that comprise binding sites (motifs) for different transcription factors (TFs). Most of the research on enhancer sequences has been focused on TF motif presence, wh...
ORGANISM(S): Homo sapiens 
2022-12-15 | GSE211657 | GEO
OtherEnhancers display sequence flexibility constrained by transcription factor motif syntax [Drosophila motif pasting STARR-seq]
The information about when and where each gene is to be expressed is mainly encoded in the DNA sequence of enhancers, sequence elements that comprise binding sites (motifs) for different transcription factors (TFs). Most of the research on enhancer sequences has been focused on TF motif presence, wh...
ORGANISM(S): Drosophila melanogaster 
2022-12-15 | GSE211654 | GEO
TranscriptomicsATAC-seq of HEK293 cells with Alu-motif targeted dCas9GFP
HEK293 cells were selected and subcloned for doxycyclin (DOX) and trimethoprim (TMP) inducible dCas9GFP and a guide RNA molecule targeting an EGA enriched Alu-motif (EEA-g1). Cells were treated with DOX and TMP for three days to induce dCas9GFP expression and ATAC-seq samples were collected from tre...
ORGANISM(S): Homo sapiens 
2018-06-07 | E-MTAB-6195 | biostudies-arrayexpress
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