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35 results for “full-length transcripts”
Supplementary Data to "Disparate regulation of Smad3 phosphorylation and collagen gene transcription by full-length IL-33"
<p>These are Supplementary Figures for the article "Disparate regulation of Smad3 phosphorylation and collagen transcription by full-length IL-33"</p>
Single molecule, full-length transcript sequencing provides insight into the extreme metabolism of ruby-throated hummingbird Archilochus colubris
<p>Hummingbirds can support their high metabolic rates exclusively by oxidizing ingested sugars, which is unsurprising given their sugar-rich nectar diet and use of energetically expensive hovering flight. However, they cannot rely on dietary sugars as a fuel during fasting periods, such as during the night, at first light, or when undertaking long-distance migratory flights, and must instead rely exclusively on onboard lipids. This metabolic flexibility is remarkable both in that the birds can switch between exclusive use of each fuel type within minutes and in that de novo lipogenesis from dietary sugar precursors is the principle way in which fat stores are built, sometimes at exceptionally high rates, such as during the few days prior to a migratory flight. The hummingbird hepatopancreas is the principle location of de novo lipogenesis and likely plays a key role in fuel selection, fuel switching, and glucose homeostasis. Yet understanding how this tissue, and the whole organism, achieves and moderates high rates of energy turnover is hampered by a fundamental lack of information regarding how genes coding for relevant enzymes differ in their sequence, expression, and regulation in these unique animals. To address this knowledge gap, we generated a de novo transcriptome of the hummingbird liver using PacBio full-length cDNA sequencing (Iso-Seq), yielding a total of 8.6Gb of sequencing data, or 2.6M reads from 4 different size fractions. We analyzed data using the SMRTAnalysis v3.1 Iso-Seq pipeline, including classification of reads and clustering of isoforms (ICE) followed by error-correction (Arrow). We performed orthology analysis to identify closely related sequences between our transcriptome and other avian and human gene sets. We also aligned our transcriptome against the Calypte anna genome where possible. Finally, we closely examined homology of critical lipid metabolic genes between our transcriptome data and avian and human genomes. We confirmed high levels of sequence divergence within hummingbird lipogenic enzymes, suggesting a high probability of adaptive divergent function in the lipogenic liver pathways. Our results have leveraged cutting-edge technology and a novel bioinformatics pipeline to provide a compelling first direct look at the transcriptome of this incredible organism.</p>
TAGET: A toolkit for analyzing full-length transcripts from long-read sequencing
<p>Polished transcripts of COLO829 from the PacBio platform. The original web link: https://downloads-ap.pacbcloud.com/public/dataset/Melanoma2019_IsoSeq/PolishedMappedTranscripts/before-SQANTI2filter/.</p>
DisFull_Lnc: discover full-length long noncoding RNAs without transcriptional initiation profiles
<p>DisFull_Lnc aims to identify full-length lncRNAs directly from raw RNA-seq data without H3K4me3 profiles from the corresponding sample.</p>
Datasets and Scripts: Full-length mRNA sequencing uncovers a widespread coupling between transcription and mRNA processing
<p>The multilayered control of gene expression requires tight coordination of regulatory mechanisms at the transcriptional and post-transcriptional level. In this study, we studied the interdependence of transcription, splicing and polyadenylation events on single mRNA molecules by full-length mRNA sequencing. In MCF-7 breast cancer cells and three human tissues, we found an unforeseen number of genes that demonstrate mutually inclusive or exclusive alternative transcription and mRNA processing events, which can span the entire length of mRNA molecules. Furthermore, alternative poly(A) sites that are coupled with alternative splicing events are depleted for known poly(A) signals and enriched for MBNL binding motifs, supporting a dual role of MBNL proteins in regulating splicing and polyadenylation. We predict thousands of open-reading frames from the sequence of full-length mRNAs, allowing for a more sensitive proteogenomics analysis of MCF-7 mass-spectrometry data. Our findings demonstrate that our understanding of transcriptome complexity is far from complete and provides a framework to reveal largely unresolved mechanisms that coordinate transcription and mRNA processing.</p>
Expression and Purification of Full-Length T-box Transcription Factor TBXTA-c027
<p>A detailed protocol for the expression and purification of G177D variant of biotinylated, full-length TBXT</p>
Data from: Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis
Astragalus membranaceus, also known as Huangqi in China, is one of the most widely used medicinal herbs in Traditional Chinese Medicine. Traditional Chinese Medicine formulations from Astragalus membranaceus have been used to treat a wide range of illnesses, such as cardiovascular disease, type 2 diabetes, nephritis and cancers. Pharmacological studies have shown that immunomodulating, anti-hyperglycemic, anti-inflammatory, antioxidant and antiviral activities exist in the extract of Astragalus membranaceus. Therefore, characterising the biosynthesis of bioactive compounds in Astragalus membranaceus, such as Astragalosides, Calycosin and Calycosin-7-O-β-D-glucoside, is of particular importance for further genetic studies of Astragalus membranaceus. In this study, we reconstructed the Astragalus membranaceus full-length transcriptomes from leaf and root tissues using PacBio Iso-Seq long reads. We identified 27 975 and 22 343 full-length unique transcript models in each tissue respectively. Compared with previous studies that used short read sequencing, our reconstructed transcripts are longer, and are more likely to be full-length and include numerous transcript variants. Moreover, we also re-characterised and identified potential transcript variants of genes involved in Astragalosides, Calycosin and Calycosin-7-O-β-D-glucoside biosynthesis. In conclusion, our study provides a practical pipeline to characterise the full-length transcriptome for species without a reference genome and a useful genomic resource for exploring the biosynthesis of active compounds in Astragalus membranaceus.
Aminoacyl-tRNA synthetase gene alignments from multiple Sileneae species generated from full-length transcripts using Iso-Seq and raw microscopy image files
<p>Trimmed and untrimmed alignments for the final aminoacyl-tRNA synthetases in <em>Sileneae </em>species and <em>Arabidopsis thaliana. W</em>e investigated the evolution of subcellular localization of aaRS enzymes in five different species from the plant lineage <em>Sileneae</em> that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts with single-molecule sequencing technology (PacBio Iso-Seq) and searching genome sequences, we found instances of predicted retargeting of an ancestrally cytosolic aaRS to the mitochondrion as well as scenarios where enzyme localization does not appear to change despite functional tRNA replacement.</p> <p>Nikon .nd2 raw microscopy files for the transient expression and imaging of predicted transit peptides and colocalization assays in <em>N. benthamiana</em> epithelial cells. The amino acid sequence plus 10 upstream amino acids of the protein body were fused to GFP and co-transfected with an eqFP611-tagged transit peptide from a known mitochondrially localized protein (isovaleryl-CoA dehydrogenase).</p>
Aminoacyl-tRNA synthetase gene alignments from multiple Sileneae species generated from full-length transcripts using Iso-Seq and raw microscopy image files
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Data from: Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis
Open the record for dataset details and reuse information.
Simultaneous profiling of full-length RNA transcripts and chromatin accessibility within single cells of human retinal organoids
GEO Series GSE251754. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
m6Am sequesters PCF11 to promote full-length transcription
GEO Series GSE234137. Homo sapiens. 99 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
m6Am sequesters PCF11 to promote full-length transcription [RNA-seq]
GEO Series GSE254148. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Benchmarking full-length transcript single cell mRNA sequencing protocols
GEO Series GSE155506. Homo sapiens. 40 samples. Type: Expression profiling by high throughput sequencing.
Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3 [HT SS3]
GEO Series GSE270928. Homo sapiens. 6415 samples. Type: Expression profiling by high throughput sequencing.
Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3 [10X]
GEO Series GSE270917. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing
GEO Series GSE150050. Homo sapiens. 28 samples. Type: Expression profiling by high throughput sequencing.
Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3 [Bulk]
GEO Series GSE270511. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Selective roles of vertebrate PCF11 in premature and full-length transcript termination
GEO Series GSE123105. Homo sapiens; Danio rerio. 95 samples. Type: Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing.
Selective roles of vertebrate PCF11 in premature and full-length transcript termination (ChIP-seq)
GEO Series GSE127256. Homo sapiens. 25 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
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.