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21,320 results for “Transcript”
Spatial integration of transcription and splicing in a dedicated compartment sustains monogenic antigen expression in African trypanosomes
<p>This repository contains the data for the manuscript <a href="https://doi.org/10.1038/s41564-020-00833-4">https://doi.org/10.1038/s41564-020-00833-4</a>.</p> <p>The HiC analysis pipeline can be found at <a href="https://github.com/bgbrink/PRJEB35632">https://github.com/bgbrink/PRJEB35632</a>.</p> <p><strong>Abstract</strong></p> <p>Highly selective gene expression is a key requirement for antigenic variation in several pathogens, allowing evasion of host immune responses and maintenance of persistent infections. African trypanosomes — parasites that cause lethal diseases in humans and livestock — employ an antigenic variation mechanism that involves monogenic antigen expression from a pool of >2,600 antigen-coding genes. In other eukaryotes, the expression of individual genes can be enhanced by mechanisms involving the juxtaposition of otherwise distal chromosomal loci in the three-dimensional nuclear space. However, trypanosomes lack classical enhancer sequences or regulated transcription initiation. In this context, it has remained unclear how genome architecture contributes to monogenic transcription elongation and transcript processing. Here, we show that the single expressed antigen-coding gene displays a specific inter-chromosomal interaction with a major messenger RNA splicing locus. Chromosome conformation capture (Hi-C) revealed a dynamic reconfiguration of this inter-chromosomal interaction upon activation of another antigen. Super-resolution microscopy showed the interaction to be heritable and splicing dependent. We found a specific association of the two genomic loci with the antigen exclusion complex, whereby VSG exclusion 1 (VEX1) occupied the splicing locus and VEX2 occupied the antigen-coding locus. Following VEX2 depletion, loss of monogenic antigen expres- sion was accompanied by increased interactions between previously silent antigen genes and the splicing locus. Our results reveal a mechanism to ensure monogenic expression, where antigen transcription and messenger RNA splicing occur in a specific nuclear compartment. These findings suggest a new means of post-transcriptional gene regulation.</p>
Transcriptions of interviews with older adults on the use of WhatsApp
<p>The file contains German transcriptions of semi-structured qualitative interviews conducted with older adults 65+ in Switzerland in 2019. The topic of the interviews was the older adults' use of the instant-messaging service WhatsApp and its perceived effects on their social relationships.</p>
Transcription initiation peaks based on FANTOM5 CAGE data on rn6, canFam3, and galGal5
<p><strong>Overview</strong></p> <p>Decomposition-based peak identification (DPI, https://github.com/hkawaji/dpi1) is applied to the FANTOM5 data of rat (rn3), dog (canFam3), and chicken (galGal5):</p> <ul> <li>https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/</li> </ul> <p>The same parameters to the ones used in the previous paper (Forrest ARR, Kawaji H, Rehli M, et al. Nature 507: 462–470, 2014) was used.</p> <p><strong>Data files</strong></p> <p>Four data files per assembly are prepared as below.</p> <ol> <li>tag cluster in the original definition (*.tc.bed.gz)</li> <li>full set of DPI peaks (*.tc.decompose_smoothing_merged.bed.gz)</li> <li>permissive set of DPI peaks (*.tc.decompose_smoothing_merged.ctssMaxCounts3.bed.gz)</li> <li>robust set of DPI peaks (*.tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.bed.gz)</li> </ol> <p><strong>Acknowledgement</strong></p> <p>This data set is supported by Research Grant from MEXT to RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Center for Integrative Medical Sciences, and JSPS KAKENHI Grant-in-Aid for Scientific Research No. 16H02902.</p>
K.1 Stele of Vằt Thlĕṅ : Transcription, translation and analysis
<p><a href="https://siddham.network/inscription/k1/">K.1</a> Stele of Vằt Thlĕṅ : Transcription, translation and analysis</p> <p><br> <a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Inscriptions+--+Cambodia">Inscriptions -- Cambodia</a><br> <a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Inscriptions.">Inscriptions. </a><br> <a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Cambodia.">Cambodia. </a></p>
K.973 Bronze Mirror Inscription : Transcription, translation and analysis
<p><a href="https://siddham.network/inscription/k973/">K.973</a> Bronze Mirror Inscription : Transcription, translation and analysis</p> <p><br> <a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Inscriptions+--+Cambodia">Inscriptions -- Cambodia</a><br> <a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Inscriptions.">Inscriptions. </a><br> <a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Cambodia.">Cambodia. </a></p> <p> </p>
K.52 Stele of Vằt Krẵṅ Svày : Transcription, translation and analysis
<p><a href="https://siddham.network/inscription/k52/">K.52</a> Stele of Vằt Krẵṅ Svày : Transcription, translation and analysis</p> <p><br> <a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Inscriptions+--+Cambodia">Inscriptions -- Cambodia</a><br> <a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Inscriptions.">Inscriptions. </a><br> <a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Cambodia.">Cambodia. </a></p>
Hassan #1 Arabic and French transcripts of description and comments on his recording in Darb al-Ahmar, Cairo (Egypt), 25-10-2011
<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>
Convolutional Neural Net (CNN) models for ENCODE-Roadmap DNase-seq peaks and Transcription Factor ChIP-seq peaks - Basset architecture
<p>Deep learning models trained on epigenomic landscapes from ENCODE and Roadmap Epigenomics. The models are Basset convolutional neural networks (Kelley, et al 2016). The dataset used to train these models can be found at https://doi.org/10.5281/zenodo.4059038. The file `nn.encode-roadmap.models.basset.clf.tar.gz` contains 10 cross-validated models in Tensorflow framework files as well as details on the architecture, cross-validation scheme, and training of these models. The file `nn.encode-roadmap.models.basset.clf.np_weights.tar.gz` contains the 10 cross-validated models' weights extracted to numpy array files (.npz).</p>
Supplementary Videos: The N-Terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition
<p>Supplementary Movies associated with the following work: "The N-Terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition", available as a preprint on chemRxiv: https://chemrxiv.org/articles/preprint/The_N-Terminal_Helix-Turn-Helix_Motif_of_Transcription_Factors_MarA_and_Rob_Drives_DNA_Recognition/12195372 </p>
Final Presentation Transcription
<p>Transcription of the final presentation.</p>
Predicting placenta transcriptional regulatory interactions based on spatial gene expression data and convolutional neural network
<p><strong>Aims:</strong> The dysfunction of placenta development is correlated to the defects of pregnancy and fetal growth. The detailed molecular mechanism of placenta development is not identified in human due to the lack of material in vivo. Image-based reconstructions of GRN are still very underdeveloped.</p> <p><strong>Methods and Results:</strong> In this study, first-trimester chorionic villus and decidua tissues were collected. Next, we present a machine-learning system to infer gene interaction networks of the human placenta from immunofluorescence images of trophoblast specific transcription factors obtained by a high-resolution scanner.</p> <p><strong>Conclusions:</strong> The experimental results show that deep learning models reveal regulatory roles that have not yet been fully recognized. The spatial expression data reveal new regulatory relationships that traditional experiments have failed to recognize, and has allowed the development of gene regulation networks based on the spatial distribution of gene expression. We demonstrate the effectiveness of this approach in building networks using high-resolution images of the human placenta. Our analysis is of certain significance for further exploration of the development of the placenta and the occurrence of pregnancy-related diseases in the future. The datasets and analysis provide a useful source for the researchers in the field of the maternal-fetal interface and the establishment of pregnancy.</p>
proportion expressed across transcripts (pext)
<p>Original file that was previously found here:</p> <pre><code class="language-http">https://storage.googleapis.com/gnomad-public/papers/2019-tx-annotation/pre_computed/all.possible.snvs.tx_annotated.022719.tsv.bgz</code></pre> <p>Now only a newer file is available:</p> <pre><code class="language-http">https://storage.googleapis.com/gnomad-public/papers/2019-tx-annotation/pre_computed/all.possible.snvs.tx_annotated.GTEx.v7.021520.tsv.bgz</code></pre> <p>which is differs from the original.</p> <p> </p> <p> </p>
Sequence data for the article "Targeted reduction of highly abundant transcripts with pseudo-random primers"
<p>Sequence data (Illumina MiSeq runs) for the article "Targeted reduction of highly abundant transcripts with pseudo-random primers". File names indicate unique run identifiers. In the manuscript, shorter names are used:</p> <ul> <li>NC12: 140602_M00528_0019_000000000-A88YD</li> <li>NC17: 140918_M00528_0047_000000000-A8GHU</li> <li>NC22b: 141105_M00528_0062_000000000-AAPC2</li> <li>NCki: 140207_M00528_0069_000000000-A5TY9</li> </ul> <p> </p>
Genome alignments for the article "Targeted reduction of highly abundant transcripts with pseudo-random primers"
<p>Sequence alignment (Moirai workflow management) for the article "Targeted reduction of highly abundant transcripts with pseudo-random primers". File names indicate unique run identifiers. In the manuscript, shorter names are used:</p> <ul> <li>NC12: NC12_1.CAGEscan_short-reads.20150629125015</li> <li>NC17: NC16-17_1.CAGEscan_short-reads.20150625154740</li> <li>NC22b: NC22b.CAGEscan_short-reads.20150625152335</li> <li>NCki: NCms10058_1.CAGEscan_short-reads.20150625154711</li> </ul>
A Small Dataset of Jazz Guitar Licks for Automatic Transcription Experiments
<p>A dataset consisting of ten (mostly monophonic) jazz guitar licks that were performed by François Pachet and recorded at the Sony Computer Science Laboratory (CSL) in Paris.</p>
རྦ་ (2011.1). Transcription of རྦ་བཞེད་ manuscript (Ziling 2011) : version 1.0
<p>This text is a transcription of the རྦ་བཞེད་ reproduced as a photo-lithograph facsimile in volume 36 of Bod gyi lo rgyus rnam thar phyogs bsgrigs gnyis pa, published from Ziling in 2011 (see TBRC W1PD153537). This text is closely related to dBa' (2000) in palaeographic terms; the narrative also corresponds up to folio 4v., after which the text breaks off and turns to events in the life of the Buddha without significant punctuation or a change in writing style. This shows that the exemplar already combined the text of the རྦ་བཞེད་ with the second text and that the subsequent parts of the narrative had already been lost in the exemplar. The present copy can be assigned to the circa fourteenth century. We refer to this as rBa (2011.1) in our publications.</p>
Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism
<ul> <li>Eight versions of COBRA-compliant SBML files are available for each Recon 2M.1 and Recon 2M.2 depending on the use of: MNXref versus BiGG IDs; Entrez gene IDs (GPR associations) versus Ensembl transcript IDs versus RefSeq transcript IDs versus UCSC transcript IDs (TPR associations for the last three database IDs).</li> <li>892 personal GEMs (only T-GEMs) built with Recon 2.2</li> <li>1,784 personal GEMs (both P-GEMs and T-GEMs) built with Recon 2M.1</li> <li>892 personal GEMs (only T-GEMs) built with Recon 2M.2</li> </ul> <p> </p> <p><strong>Publication</strong></p> <p>Jae Yong Ryu<sup>1</sup>, Hyun Uk Kim<sup>1</sup> & Sang Yup Lee<sup>*</sup>. Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism., <em>Proc. Natl. Acad. Sci. U.S.A.</em>, 2017, http://www.pnas.org/content/early/2017/10/23/1713050114</p> <p> </p>
A cross-study transcriptional patient map of heart failure defines conserved multicellular coordination in cardiac remodeling
<p>Collection of auxiliary data to reproduce the results from "<strong>A cross-study transcriptional patient map of heart failure defines conserved multicellular coordination in cardiac remodeling</strong>". Source code is available at: https://github.com/saezlab/reheat2_pub<br><br>We provide processed data to facilitate access to the results, for the original count data, please see the associated manuscript for references to the original datasets. </p> <p> </p> <p> </p>
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark
<p>In this repository, we present the PacBio and ONT simulated datasets used for benchmarking transcriptome reconstruction tools, as evaluated in the manuscript titled "<i>SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark</i>". The dataset includes simulated long reads, short reads, CAGE peaks, and a reduced reference annotation. Additionally, we have included reconstructed transcriptomes from each method, along with SQANTI3 output files. The SQANTI-SIM software can be accessed on GitHub at the following URL: <a href="https://github.com/ConesaLab/SQANTI-SIM">https://github.com/ConesaLab/SQANTI-SIM</a>.</p>
Transcriptional profiling of peripheral blood mononuclear cells identifies inflammatory phenotypes in ataxia telangiectasia
<p>This is an AnnData object in h5ad (hdf5) format containing de-identified bulk RNA-seq gene expression matrices from PBMCs. These data are related to the study entitled "Transcriptional profiling of peripheral blood mononuclear cells identifies inflammatory phenotypes in ataxia telangiectasia". </p><p>This AnnData object contains a table of sample-specific metadata (`obs`), gene-specific metadata (`var`), and multiple gene expression matrices stored as `layers`. These layers include raw counts, DEseq2 normalized counts, vst normalized counts, and rlog normalized counts. Some additional layers include regressed versions of the previously mentioned counts matrices, where sequencing batch (`cohort` in the obs table) has been regressed out using the `combat` tool. The layer `rlog_combat_regressed_batch` is recommended for downstream processing, and has been loaded into the `X` slot of the anndata object for convenience. </p><p>The md5sum of this h5ad file is listed here: 04d7c6c549fb37cf730a5dca7897f86f</p><p>Opening and working with AnnData objects in h5ad format requires the use of the `anndata` python library (https://github.com/scverse/anndata). </p>
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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.