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21,320 results for “Transcription”
Hassan #2 Arabic and French transcripts of description and comments on his recording in Duwiqa, Cairo (Egypt), 28-09-2012
<p>« Mics in the Ears » binaural experiment in Cairo (Egypt): Vincent Battesti & Nicolas Puig, social anthropologists, asked inhabitants of Cairo megapolis in Egypt to record the surrounding urban sounds during one of their daily journeys (without the researcher), equipped with binaural microphones and GPS device. Participants have recorded in different Cairo neighbourhoods, and are themselves from different generations, social and economic backgrounds, and different genders.</p> <p>These text files (pdf and Word) are the transcripts (original in Arabic and translation in French) of the audio file of the description and comments one of them gave us a posteriori when listening to his/her own route he/she recorded with binaural mics. See https://vbat.org/article831</p>
Salma Arabic and French transcripts of description and comments on her recording in Wast al-Balad, Cairo (Egypt), 26-09-2012
<p>« Mics in the Ears » binaural experiment in Cairo (Egypt): Vincent Battesti & Nicolas Puig, social anthropologists, asked inhabitants of Cairo megapolis in Egypt to record the surrounding urban sounds during one of their daily journeys (without the researcher), equipped with binaural microphones and GPS device. Participants have recorded in different Cairo neighbourhoods, and are themselves from different generations, social and economic backgrounds, and different genders.</p> <p>These text files (pdf and Word) are the transcripts (original in Arabic and translation in French) of the audio file of the description and comments one of them gave us a posteriori when listening to his/her own route he/she recorded with binaural mics. See https://vbat.org/article831</p>
Mohammed Arabic and French transcripts of description and comments on his recording in Ghamra, Cairo (Egypt), 30-05-2013
<p>« Mics in the Ears » binaural experiment in Cairo (Egypt): Vincent Battesti & Nicolas Puig, social anthropologists, asked inhabitants of Cairo megapolis in Egypt to record the surrounding urban sounds during one of their daily journeys (without the researcher), equipped with binaural microphones and GPS device. Participants have recorded in different Cairo neighbourhoods, and are themselves from different generations, social and economic backgrounds, and different genders.</p> <p>These text files (pdf and Word) are the transcripts (original in Arabic and translation in French) of the audio file of the description and comments one of them gave us a posteriori when listening to his/her own route he/she recorded with binaural mics. See https://vbat.org/article831</p>
Shady Arabic and French transcripts of description and comments on his recording in Wast al-Balad, Cairo (Egypt), 26-09-2012
<p>« Mics in the Ears » binaural experiment in Cairo (Egypt): Vincent Battesti & Nicolas Puig, social anthropologists, asked inhabitants of Cairo megapolis in Egypt to record the surrounding urban sounds during one of their daily journeys (without the researcher), equipped with binaural microphones and GPS device. Participants have recorded in different Cairo neighbourhoods, and are themselves from different generations, social and economic backgrounds, and different genders.</p> <p>These text files (pdf and Word) are the transcripts (original in Arabic and translation in French) of the audio file of the description and comments one of them gave us a posteriori when listening to his/her own route he/she recorded with binaural mics. See https://vbat.org/article831</p>
Samir Arabic and French transcripts of description and comments on his recording in Bashtil, Cairo (Egypt), 28-09-2012
<p>« Mics in the Ears » binaural experiment in Cairo (Egypt): Vincent Battesti & Nicolas Puig, social anthropologists, asked inhabitants of Cairo megapolis in Egypt to record the surrounding urban sounds during one of their daily journeys (without the researcher), equipped with binaural microphones and GPS device. Participants have recorded in different Cairo neighbourhoods, and are themselves from different generations, social and economic backgrounds, and different genders.</p> <p>These text files (pdf and Word) are the transcripts (original in Arabic and translation in French) of the audio file of the description and comments one of them gave us a posteriori when listening to his/her own route he/she recorded with binaural mics. See https://vbat.org/article831</p>
Maurice Arabic and French transcripts of description and comments on his recording in Garden City, Cairo (Egypt), 30-05-2013
<p>« Mics in the Ears » binaural experiment in Cairo (Egypt): Vincent Battesti & Nicolas Puig, social anthropologists, asked inhabitants of Cairo megapolis in Egypt to record the surrounding urban sounds during one of their daily journeys (without the researcher), equipped with binaural microphones and GPS device. Participants have recorded in different Cairo neighbourhoods, and are themselves from different generations, social and economic backgrounds, and different genders.</p> <p>These text files (pdf and Word) are the transcripts (original in Arabic and translation in French) of the audio file of the description and comments one of them gave us a posteriori when listening to his/her own route he/she recorded with binaural mics. See https://vbat.org/article831</p>
Evelyn Arabic and French transcripts of description and comments on her recording in Wast al-Balad, Cairo (Egypt), 29-05-2013
<p>« Mics in the Ears » binaural experiment in Cairo (Egypt): Vincent Battesti & Nicolas Puig, social anthropologists, asked inhabitants of Cairo megapolis in Egypt to record the surrounding urban sounds during one of their daily journeys (without the researcher), equipped with binaural microphones and GPS device. Participants have recorded in different Cairo neighbourhoods, and are themselves from different generations, social and economic backgrounds, and different genders.</p> <p>These text files (pdf and Word) are the transcripts (original in Arabic and translation in French) of the audio file of the description and comments one of them gave us a posteriori when listening to his/her own route he/she recorded with binaural mics. See https://vbat.org/article831</p>
Integron array MICs and cassettes transcription data
<p>Mobile integrons are widespread genetic platforms that allow bacteria to modulate the expression of antibiotic resistance cassettes by shuffling their position from a common promoter. Antibiotic stress induces the expression of an integrase that excises and integrates cassettes, and this unique recombination and expression system is thought to allow bacteria to 'evolve on demand' in response to antibiotic pressure. To test this hypothesis, we inserted a custom three cassette integron into <em>P. aeruginosa</em>, and used experimental evolution to measure the impact of integrase activity on adaptation to gentamicin. Crucially, integrase activity accelerated evolution by increasing the expression of a gentamicin resistance cassette through duplications and by eliminating redundant cassettes. Importantly, we found no evidence of deleterious off-target effects of integrase activity. Our results show that integrons accelerate resistance evolution by rapidly generating combinatorial variation in cassette composition while maintaining genomic integrity, and they highlight the importance of semi-conservative cassette excision for integron dynamics.</p>
ScaR — a tool for sensitive detection of known fusion transcripts
<p>Use scaffold re-aligning approach to detect the prevalence and recurrence of known fusion transcripts across samples</p>
Screening for functional transcriptional and splicing regulatory variants with GenIE
<p>Here we provide data used in the analysis for our paper introducing the GenIE method (Genome engineering-based Interrogation of Enhancers).</p> <p><strong>Abstract</strong></p> <p>Genome-wide association studies (GWAS) have identified numerous genetic loci underlying human diseases, but a fundamental challenge remains to accurately identify the underlying causal genes and variants. Here we describe an arrayed CRISPR screening method, Genome engineering-based Interrogation of Enhancers (GenIE), which assesses the effects of defined alleles on transcription or splicing when introduced in their endogenous genomic location. We use this sensitive assay to validate the activity of transcriptional enhancers and splice regulatory elements in human induced pluripotent stem cells (hiPSCs), and develop a software package (rgenie) to analyse the data. We screen the 99% credible set of Alzheimer’s disease (AD) GWAS variants identified at the clusterin (CLU) locus to identify a subset of likely causal variants, and employ GenIE to understand the impact of specific mutations on splicing efficiency. We thus establish GenIE as an efficient tool to rapidly screen for the role of transcribed variants on gene expression.</p>
Classification dataset for ENCODE-Roadmap DNase-seq peaks and Transcription Factor ChIP-seq peaks
<p>Classification dataset for machine learning on epigenomic landscapes from ENCODE and Roadmap Epigenomics. The dataset includes the original peak files (BED format) for the DNase-seq and transcription factor (TF) ChIP-seq experiments that were used to label genomic regions as positives or negatives. The DNase-seq peak files along with processing details are in the file "encode-roadmap.DNase-seq.peaks.tar.gz". The TF ChIP-seq peak files along with processing details are in the file "encode.ChIP-seq.peaks.tar.gz". The processed dataset stored in hdf5 format files along with processing details are in the file "nn.encode-roadmap.hdf5_files.tar.gz".</p>
The strength and form of natural selection on transcript abundance in the wild
<p>Gene transcription variation is known to contribute to disease susceptibility and adaptation, but we currently know very little about how contemporary natural selection shapes transcript abundance. Here, we propose a novel analytical framework to quantify the strength and form of ongoing natural selection at the transcriptome level in a wild vertebrate. We estimated selection on transcript abundance in a cohort of a wild salmonid fish (<i>Salmo trutta</i>) affected by an extracellular myxozoan parasite (<i>Tetracapsuloides bryosalmonae</i>) through mark-recapture field sampling and the integration of RNA-seq with classical regression-based selection analysis. We show, based on fin transcriptomes of the host, that infection by the parasite and subsequent host survival is linked to upregulation of mitotic cell cycle process. We also detect a <span class="Heading3Char">widespread signal of disruptive selection</span> on transcripts linked to host immune defence, host-pathogen interactions, cellular repair and maintenance. Our results provide insights about how selection can be measured at the transcriptome level to dissect the molecular mechanisms of contemporary natural selection driven by climate change and emerging anthropogenic threats. We anticipate that the approach described here will enable critical information on the molecular mechanisms and targets of natural selection to be obtained in real time.</p>
PCB126 exposure revealed alterations in m6A RNA modifications in transcripts associated with AHR activation
<p>Chemical modifications of proteins, DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests the RNA modifications (epitranscriptomics) have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is <i>N</i><sup>6</sup>-methyladenosine (m6A). In a subset of mRNAs, m<sup>6</sup>A sites are preferentially enriched near stop codons, in 3′ UTRs, and within exons, suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes, it is important to understand the effects of exposure on this important layer of gene regulation. Hence, the objective of this study was to characterize the acute effects of developmental exposure to PCB126, an environmentally relevant dioxin-like PCB, on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for 6 hours starting from 72 hours post-fertilization and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Our analysis revealed 117 and 217 m6A peaks in the DMSO and PCB126 samples (FDR 5%), respectively. The majority of the peaks were preferentially located around the 3'UTR and stop codons. Statistical analysis revealed 15 m6A marked transcripts to be differentially methylated by PCB126 exposure. These include transcripts that are known to be activated by AHR agonists (e.g., <i>ahrra</i>, <i>tiparp</i>, <i>nfe2l2b) as well as others that are important for normal development (vgf, cebpd, sned1). These results suggest that</i> environmental chemicals such as dioxin-like PCBs could affect developmental gene expression patterns by altering m6A levels. Further studies are necessary to understand the functional consequences of exposure-associated alterations in m6A levels.</p>
Analysis and Figures from "Causal network inference from gene transcriptional time-series response to glucocorticoids"
<p>Gene regulatory network inference is essential to uncover complex relationships among gene pathways and inform downstream experiments, ultimately enabling regulatory network re-engineering. Network inference from transcriptional time-series data requires accurate, interpretable, and efficient determination of causal relationships among thousands of genes. Here, we develop Bootstrap Elastic net regression from Time Series (BETS), a statistical framework based on Granger causality for the recovery of a directed gene network from transcriptional time-series data. BETS uses elastic net regression and stability selection from bootstrapped samples to infer causal relationships among genes. BETS is highly parallelized, enabling efficient analysis of large transcriptional data sets. We show competitive accuracy on a community benchmark, the DREAM4 100-gene network inference challenge, where BETS is one of the fastest among methods of similar performance and additionally infers whether the causal effects are activating or inhibitory. We apply BETS to transcriptional time-series data of 2,768 differentially-expressed genes from A549 cells exposed to glucocorticoids over a period of 12 hours. We identify a network of 2,768 genes and 31,945 directed edges (FDR <= 0.2). We validate inferred causal network edges using two external data sources: overexpression experiments on the same glucocorticoid system, and genetic variants associated with inferred edges in primary lung tissue in the Genotype-Tissue Expression (GTEx) v6 project. BETS is available as an open source software package at https://github.com/lujonathanh/BETS</p> <p>This upload documents the analysis and figure files that support each numerical claim of the manuscript. Full Progeny.xlsx lists out the relevant code and files for each numerical claim of the manuscript, assuming the home folder of port-from-della</p>
Data from: Severe childhood speech disorder: Gene discovery highlights transcriptional dysregulation
<p><b><span>Objective:</span></b><span> Determining the genetic basis of speech disorders provides insight into the neurobiology of human communication. Despite intensive investigation over the past two decades, the etiology of most children with speech disorder remains unexplained. Here we </span>searched for a genetic etiology in children with severe speech disorder, specifically childhood apraxia of speech (CAS).</p> <p><b>Methods:</b> Precise phenotyping together with research genome or exome analysis were performed on children referred with a primary diagnosis of CAS, as well as other medical or neurodevelopmental co-morbidities. Gene co-expression and gene set enrichment analyses analyses were conducted on high confidence gene candidates.</p> <p><b>Results:</b> 34 probands ascertained for CAS were studied. In 11/34 (32%) probands, we identified highly plausible pathogenic single nucleotide (n=10, <i>CDK13, EBF3, GNAO1, GNB1, DDX3X, MEIS2, POGZ, SETBP1, UPF2, ZNF142</i>) or copy number (n = 1, 5q14.3q21.1 locus) variants in novel genes or loci for CAS. Testing of parental DNA was available for nine probands and confirmed that the variants had arisen <i>de novo</i>. Eight genes encode proteins critical for regulation of gene transcription, and analyses of transcriptomic data found CAS-implicated genes were highly co-expressed in the developing human brain.</p> <p><b>Conclusion:</b><i> </i>We identify the likely genetic aetiology in 11 patients with CAS and implicate 9 genes for the first time. We find that CAS is often a sporadic monogenic disorder, and highly genetically heterogeneous. Highly penetrant variants implicate shared pathways in broad transcriptional regulation, highlighting the key role of transcriptional regulation in normal speech development. CAS is a distinctive, socially debilitating clinical disorder, and understanding its molecular basis is the first step towards identifying precision medicine approaches.</p>
Detection of fusion transcripts and their genomic breakpoints from RNA sequencing data - Table S03 - All detected SVs.xlsx
<p>Large concatenated results table on all samples of the Dr. Disco study.</p> <p> </p>
DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon
<p>Supplementary Information for the manuscript: "DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon"</p>
Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup
<p>Positive supercoiling buildup (PSB) is a pervasive phenomenon in the transcriptional programs of Escherichia coli. After finding a range of Gyrase concentrations where the inverse of the transcription rate of a chromosome-integrated gene changes linearly with the inverse of Gyrase concentration, we apply a Line Weaver-Burk plot to dissect the expected in vivo transcription rate in absence of PSB. We validate the estimation by time-lapse microscopy of single-RNA production kinetics of the same gene when single-copy plasmid-borne, shown to be impervious to Gyrase inhibition. Next, we estimate the fraction of time in locked states and number of transcription events prior to locking, which we validate by measurements under Gyrase inhibition. Replacing the gene of interest by one with slower transcription rate decreases the fraction of time in locked states due to PSB. Finally, we combine data from both constructs to infer a range of possible transcription initiation locking kinetics in a chromosomal location, obtainable by tuning the transcription rate. We validate with measurements of transcription activity at different induction levels. This strategy for dissecting transcription initiation locking kinetics due to PSB can contribute to resolve the transcriptional programs of E. coli and in the engineering of synthetic genetic circuits.</p>
Transitions in paternal social status predict patterns of offspring growth and metabolic transcription
Parental effects occur when changes in the parental phenotype or environment cause changes to offspring phenotype. While some parental effects are triggered in response to an environmental cue in a time-locked fashion, other parental effects persist even after the cue has been removed, suggesting multiple timescales of action. For parental effects to serve as reliable signals of current environmental conditions, they should be reversible, such that when the cue changes, offspring phenotypes change in accordance. Social hierarchy is a prevalent feature of the environment, and current parental social status could signal the environment in which offspring will be born. Here, we sought to address parental effects of social status and their timescale of action in mice. We show that competition in seminatural environments affects offspring growth rate. Although dominant males are not heavier than nondominant or control males, they produce faster growing offspring, particularly sons. The timing, effect-size, and sex-specificity of this association are modulated by maternal social experience. We show that a change in paternal social status is sufficient to modulate offspring weight: from one breeding cycle to the next, status-ascending males produce heavier sons than before, and status-descending males produce lighter sons than before. Current paternal status is also highly predictive of liver transcription in sons, including molecular pathways controlling oxidative phosphorylation and iron metabolism. These results are consistent with a parental effect of social experience, although alternative explanations are considered. In summary, changes in paternal social status are associated with changes in offspring growth and metabolism.
HAND2 Targets Define a Network of Transcriptional Regulators that Compartmentalize the Early Limb Bud Mesenchyme
<p>Highlights</p> <p>•</p> <p>ChIP-seq identifies the CRMs bound by endogenous HAND2 in embryos and limb buds</p> <p>•</p> <p>HAND2 controls key transcriptional regulators acting upstream of SHH in limb buds</p> <p>•</p> <p>These transcriptional circuits define proximal, anterior, and posterior identities</p> <p>•</p> <p>HAND2 establishes anterior and posterior compartments by regulating <em>Gli3</em> and <em>Tbx3</em></p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.