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134 results for “promoter sequence”
Dataset to the publication "A unique signal sequence of the chemokine receptor CCR7 promotes package into COPII vesicles for efficient receptor trafficking"
<p>This repository accompanies the paper:</p> <p>"A unique signal sequence of the chemokine receptor CCR7 promotes package into COPII vesicles for efficient receptor trafficking".</p> <p>Organized into 14 folders it provides the data allowing the replication of all analyses and the manuscript's figures. For a more convenient download files were zipped.</p> <p>Upon publication of results using this dataset, please cite the following paper:</p> <p>Uetz-von Allmen E, Rippl AV, Farhan H, Legler DF. 2018. A unique signal sequence of the chemokine receptor CCR7 promotes package into COPII vesicles for efficient receptor trafficking. J Leukoc Biol 104(2):375-389.</p>
Data from: High-throughput mRNA sequencing-based DEGs: HNF4A mitigates sepsis-associated lung injury by upregulating NCOR2/GR/STAB1 axis and promoting macrophage polarization towards M2 phenotype
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RNA sequencing of PET127 mutants overexpressed using the galactose inducible promoter
<p>In Saccharomyces cerevisiae, <em>PET127</em> is a mitochondrial RNA exonuclease known to interact with the mitochondrial RNA polymerase <em>RPO41</em>. The nature of the interaction between <em>PET127</em> and <em>RPO41</em> is unclear. Here, we overexpressed different <em>PET127</em> mutants for five hours utilizing the galactose inducible promoter on high-copy plasmids, collected samples, and performed RNA sequencing to understand the mitochondrial RNA landscape in each condition. The mutants tested were <em>PET127</em> lacking the nuclease activity (<em>pet127-nd</em>) and two truncated forms of <i>PET127</i>: either lacking the <em>RPO41</em> binding region (<i>pet127∆(48-215</i>)), or only containing the <i>RPO41</i> binding region (<em>pet127(1-215)</em>).</p>
RNA sequencing of PET127 mutants overexpressed using the galactose inducible promoter
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Data from: Plasticity of promoter-core sequences allows bacteria to compensate for the loss of a key global regulatory gene
Transcription regulatory networks (TRNs) are of central importance for both short-term phenotypic adaptation in response to environmental fluctuations and long-term evolutionary adaptation, with global regulatory genes often being targets of natural selection in laboratory experiments. Here, we combined evolution experiments, whole-genome resequencing, and molecular genetics to investigate the driving forces, genetic constraints, and molecular mechanisms that dictate how bacteria can cope with a drastic perturbation of their TRNs. The crp gene, encoding a major global regulator in Escherichia coli, was deleted in four different genetic backgrounds, all derived from the Long-Term Evolution Experiment (LTEE) but with different TRN architectures. We confirmed that crp deletion had a more deleterious effect on growth rate in the LTEE-adapted genotypes; and we showed that the ptsG gene, which encodes the major glucose-PTS transporter, gained CRP dependence over time in the LTEE. We then further evolved the four crp-deleted genotypes in glucose minimal medium, and we found that they all quickly recovered from their growth defects by increasing glucose uptake. We showed that this recovery was specific to the selective environment and consistently relied on mutations in the cis regulatory region of ptsG, regardless of the initial genotype. These mutations affected the interplay of transcription factors acting at the promoters, changed the intrinsic properties of the existing promoters, or produced new transcription initiation sites. Therefore, the plasticity of even a single promoter region can compensate by three different mechanisms for the loss of a key regulatory hub in the E. coli TRN.
Data from: miR-122, small RNA annealing and sequence mutations alter the predicted structure of the Hepatitis C virus 5′ UTR RNA to stabilize and promote viral RNA accumulation
Annealing of the liver-specific microRNA, miR-122, to the Hepatitis C virus (HCV) 5′ UTR is required for efficient virus replication. By using siRNAs to pressure escape mutations, 30 replication-competent HCV genomes having nucleotide changes in the conserved 5′ untranslated region (UTR) were identified. In silico analysis predicted that miR-122 annealing induces canonical HCV genomic 5′ UTR RNA folding, and mutant 5′ UTR sequences that promoted miR-122-independent HCV replication favored the formation of the canonical RNA structure, even in the absence of miR-122. Additionally, some mutant viruses adapted to use the siRNA as a miR-122-mimic. We further demonstrate that small RNAs that anneal with perfect complementarity to the 5′ UTR stabilize and promote HCV genome accumulation. Thus, HCV genome stabilization and life-cycle promotion does not require the specific annealing pattern demonstrated for miR-122 nor 5′ end annealing or 3′ overhanging nucleotides. Replication promotion by perfect-match siRNAs was observed in Ago2 knockout cells revealing that other Ago isoforms can support HCV replication. At last, we present a model for miR-122 promotion of the HCV life cycle in which miRNA annealing to the 5′ UTR, in conjunction with any Ago isoform, modifies the 5′ UTR structure to stabilize the viral genome and promote HCV RNA accumulation.
Carbazole derivatives binding to Bcl-2 promoter sequence G-quadruplex
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Data from: miR-122, small RNA annealing and sequence mutations alter the predicted structure of the Hepatitis C virus 5′ UTR RNA to stabilize and promote viral RNA accumulation
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Data from: Plasticity of promoter-core sequences allows bacteria to compensate for the loss of a key global regulatory gene
Open the record for dataset details and reuse information.
Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors (protein binding microarray data set)
GEO Series GSE110653. Drosophila melanogaster. 2 samples. Type: Genome binding/occupancy profiling by array.
TET-catalyzed 5-carboxylcytosine promotes CTCF binding to suboptimal sequences genome-wide
GEO Series GSE123101. Mus musculus. 20 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
single-cell RNA transcriptome sequencing revealed that androgen/AR signaling promotes neutrophil precursors proliferation in bone marrow
GEO Series GSE198175. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
Promoter DNA sequence guides factors that position the +1 nucleosome and facilitate TBP binding [array]
GEO Series GSE98205. Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C; Saccharomyces cerevisiae W303. 12 samples. Type: Expression profiling by array.
RNA-Sequencing and promoter chromatin profiles analysis of High Glucose Treated Monocytes
GEO Series GSE43871. Homo sapiens. 20 samples. Type: Genome binding/occupancy profiling by genome tiling array; Expression profiling by high throughput sequencing.
Screening of a novel strong promoter by RNA sequencing and its application to H2 production in a hyperthermophilic archaeon
GEO Series GSE64036. Thermococcus onnurineus NA1. 2 samples. Type: Expression profiling by high throughput sequencing.
Probing the effect of promoters on noise in gene expression using thousands of designed sequences
GEO Series GSE55346. synthetic construct. 2 samples. Type: Other.
Sequencing to Explore the Mechanism Network of N-acetyltransferase 10 (NAT10) Promoting Colorectal cancer in human colorectal cancer cell SW620 [ac4CRIP]
GEO Series GSE265993. Homo sapiens. 12 samples. Type: Other.
4C-seq indicate interactive sites with the sequence close from Meis2 promoter
GEO Series GSE52281. Mus musculus. 1 samples. Type: Other.
The Upstream Sequence Transcription Complex Dictates Nucleosome Positioning and Promoter Accessibility at piRNA Genes in the C. elegans germ line [ChIP-Seq]
GEO Series GSE232141. Caenorhabditis elegans. 52 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Compatibility logic of human enhancer and promoter sequences
GEO Series GSE184426. Homo sapiens. 128 samples. Type: Other.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.