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21,320 results for “Transcription”
Transcription of interviews in Home Care
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Multimodal single-cell analyses reveal distinct fusion-regulated transcriptional programs in Ewing sarcoma.
<p>All processed data for analysis at <a href="https://github.com/furlan-lab/EwS_multiome">https://github.com/furlan-lab/EwS_multiome</a></p>
Fig. 4 in Successful transcription but not translation or assembly of Solenopsis invicta virus 3 in a baculovirus-driven expression system
Fig. 4. Quantitative PCR (absolute) results evaluating transcript production of SINV-3 by AcSINV-3-infected Sf21 cells. RNA preparations from AcSINV-3 (2 rep- licates, Ci and Di) were treated with DNase I, reverse transcribed, and amplified by qPCR. Results were compared with a series of plasmid constructs containing a portion of the SINV-3 genome (102–109 genome equivalents). The region amplified was at the 3'-most end of ORF2 (see Fig. 2). No amplification was detected in polyhedrin-negative AcRP23.lacZ preparations.
RNA isolation and reverse transcription–polymerase chain reaction, AND ChIP assay
<p>RNA isolation and reverse transcription–polymerase chain reaction, AND ChIP assay</p>
Alignment and mapping methodology impact transcript abundance estimation
<pre>SRR109.txt -> list of accession numbers used for experimental analysis. simulatedquants -> Bowtie2 pipeline quantification results on the 109 samples, that are used to simulate datasets for futher analysis. scriptsSimulate -> scripts to generate simulated data using the 109 quantification results on real data. The "runme.sh" file can be executed to generate a "data" folder with all the simulated reads and ground truth count and TPM values. table1Data -> fasta and true abundance files for 10 replicates of simulated data (from human transcriptome GENCODE v29) used to generate table 1 of the manuscript. table2Data -> fasta and true abundance files for 10 replicates of simulated data (from mouse transcriptome PWK variant) used to generate table 2 of the manuscript. refFastas -> the human and mouse reference fasta files containing the sequence-similar decoy sequences, which can be used to construct the salmon index for SA.</pre>
Supplementary Material Requirements Study - Identifying Necessary Green Coding Knowledge for Young Professionals Starting their Careers in the Software Industry Full Audio Transcript with transcribers Notes
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Highly multiplexed design of an allosteric transcription factor to sense novel ligands
<p>Processed datasets for Sensor-seq analysis</p>
Transcript of Interview - Case study
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Transcriptional conservation and innovation of cell types across mammalian hypothalamus development
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Transcript Strategic Alliances as a Catalyst for Sustainable Growth: A Case Study of the Indonesian Cosmetics Industry
<p>Consist of interview guide, transcript, code, triangulation and research protocol</p>
Data for Single-molecule Detection of Modified Amino Acid Regulating Transcriptional Activity
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Dataset Coded transcript Student Mobility and Career Advancement
<p>Dataset Transcript Student Mobility and Career Advancement </p>
Data for "Transcriptional Diversification in a Human-Adapting Zoonotic Pathogen Drives Niche-Specific Evolution"
<div> <p>This repository contains the data and codes for reproducing results and figures in the associated manuscript:</p> <p>Transcriptional Diversification in a Human-Adapting Zoonotic Pathogen Drives Niche-Specific Evolution</p> </div>
FIG. 1 in High-quality herbarium-label transcription by citizen scientists improves taxonomic and spatial representation of the tropical plant family Annonaceae
FIG. 1. — Label of specimen P02032119, illustrating some challenges of deciphering specimen labels. Collected by Pobéguin in 1895. No s.n., Isolona calycina Pierre, nomen nudum in herb. (never validly published). "Le calice y est 2 fois plus longue et plus large que chez les autres espèces" [The calyx here is two times longer and wider than in the other species]. "Hab. Côte de l'Ivoire. Cult in H[ortus] B[otanicus] M[usei] Par[isiensis] 4/1905. Floret [blossoms]" (referring to the sampling of the specimen in 1905).
FIG. 3 in High-quality herbarium-label transcription by citizen scientists improves taxonomic and spatial representation of the tropical plant family Annonaceae
FIG. 3. — Spatial distribution and density of Annonaceae records transcribed by the 'Herbonautes' citizen science project, grouped by specimens (A, an individual specimen being defined as a single barcoded sheet), by species (B) and by botanical collectors (C), log scaled, grid resolution 1 × 1° (c. 110 × 110 km at the equator), equirectangular (EPSG 4326) projection.
FIG. 2 in High-quality herbarium-label transcription by citizen scientists improves taxonomic and spatial representation of the tropical plant family Annonaceae
FIG. 2. — Cumulative percentage of specimens representing percentage of species, by dataset. The dashed line with grey boxes represents the Herbonautes dataset, continuous line with white boxes represent the GBIF dataset.
Data from: Fusion transcript discovery in formalin-fixed paraffin-embedded human breast cancer tissues reveals a link to tumor progression
The identification of gene fusions promises to play an important role in personalized cancer treatment decisions. Many rare gene fusion events have been identified in fresh frozen solid tumors from common cancers employing next-generation sequencing technology. However the ability to detect transcripts from gene fusions in RNA isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissues, which exist in very large sample repositories for which disease outcome is known, is still limited due to the low complexity of FFPE libraries and the lack of appropriate bioinformatics methods. We sought to develop a bioinformatics method, named gFuse, to detect fusion transcripts in FFPE tumor tissues. An integrated, cohort based strategy has been used in gFuse to examine single-end 50 base pair (bp) reads generated from FFPE RNA-Sequencing (RNA-Seq) datasets employing two breast cancer cohorts of 136 and 76 patients. In total, 118 fusion events were detected transcriptome-wide at base-pair resolution across the 212 samples. We selected 77 candidate fusions based on their biological relevance to cancer and supported 61% of these using TaqMan assays. Direct sequencing of 19 of the fusion sequences identified by TaqMan confirmed them. Three unique fused gene pairs were recurrent across the 212 patients with 6, 3, 2 individuals harboring these fusions respectively. We show here that a high frequency of fusion transcripts detected at the whole transcriptome level correlates with poor outcome (P<0.0005) in human breast cancer patients. This study demonstrates the ability to detect fusion transcripts as biomarkers from archival FFPE tissues, and the potential prognostic value of the fusion transcripts detected.
Data from: Environmental associations with gene transcription in Babine Lake rainbow trout: evidence for local adaptation
The molecular genetic mechanisms facilitating local adaptation in salmonids continue to be poorly characterized. Gene transcription is a highly regulated step in the expression of a phenotype and it has been shown to respond to selection and thus may be one mechanism that facilitates the development of local adaptation. Advances in molecular genetic tools and an increased understanding of the functional roles of specific genes allow us to test hypotheses concerning the role of variable environments in shaping transcription at known-function candidate loci. To address these hypotheses, wild rainbow trout were collected in their first summer and subjected to metabolic and immune challenges. We assayed gene transcription at candidate loci that play a role in the molecular genetic response to these stresses, and correlated transcription with temperature data from the streams and the abundance and diversity of bacteria as characterized by massively parallel pyrosequencing. Patterns of transcriptional regulation from resting to induced levels varied among populations for both treatments. Co-inertia analysis demonstrated significant associations between resting levels of metabolic gene transcription and thermal regime (R2 = 0.19, P = 0.013) as well as in response to challenge (R2 = 0.39, P = 0.001) and resting state and challenged levels of cytokine gene transcription with relative abundances of bacteria (resting: R2 = 0.25, P = 0.009, challenged: R2 = 0.65, P = 0.001). These results show that variable environments, even within a small geographic range (<250 km), can drive divergent selection among populations for transcription of genes related to surviving stress.
Rice genome-scale network integration reveals transcriptional regulators of grass cell wall synthesis
<p><span><span><span><span><span><span><span><span><span><span><span>Grasses have evolved distinct cell wall composition and patterning relative to dicotyledonous plants. However, despite the importance of this plant family, transcriptional regulation of its cell wall biosynthesis is poorly understood. To identify grass cell wall-associated transcription factors, we constructed the Rice Combined mutual Ranked Network (RCRN). The RCRN covers >90% of annotated rice (<i>Oryza sativa</i>) genes, is high quality, and includes most grass-specific cell wall genes, such as mixed-linkage glucan synthases and hydroxycinnamoyl acyltransferases. Comparing the RCRN and an equivalent <i>Arabidopsis </i>network suggests that grass orthologs of most genetically verified eudicot cell wall regulators also control this process in grasses, but some vary significantly in network connectivity between these divergent species. Reverse genetics, yeast-one-hybrid, and protoplast-based assays reveal that OsMYB61a activates a grass-specific acyltransferase promoter, which confirms network predictions and supports grass-specific cell wall synthesis genes being incorporated into conserved regulatory circuits. In addition, 10 of 15 tested transcription factors, including six novel <u>w</u>all-<u>a</u>ssociated regulators (WAP1, WACH1, WAHL1, WADH1, OsMYB13a, and OsMYB13b), alter abundance of cell wall-related transcripts when transiently expressed. The results highlight the quality of the RCRN for examining rice biology, provide insight into the evolution of cell wall regulation, and identify network nodes and edges that are possible leads for improving cell wall composition.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster
Here we present a statistically rigorous approach to quantifying microarray expression data that allows the relative effects of multiple classes of treatment to be compared and incorporates analytical methods that are common to quantitative genetics. From the magnitude of gene effects and contributions of variance components, we find that gene expression in adult flies is affected most strongly by sex, less so by genotype and only weakly by age (for 1- and 6-wk flies); in addition, sex x genotype interactions may be present for as much as 10% of the Drosophila transcriptome. This interpretation is compromised to some extent by statistical issues relating to power and experimental design. Nevertheless, we show that changes in expression as small as 1.2-fold can be highly significant. Genotypic contributions to transcriptional variance may be of a similar magnitude to those relating to some quantitative phenotypes and should be considered when assessing the significance of experimental treatments.
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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.