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doi: 10.1371/journal.pcbi.1009194. Data Descriptor: Single cell RNAseq of mouse brain and lung vascular and vessel-associated cell types. We also determined the transcriptome in each tissue or cell type through RNA-Seq experiments using a protocol that permits the detection of both abundance and strandedness of RNA transcripts. The workflow of database generation and web-tool implementation are shown. 2016; 17:1–12. Binds to nascent pre-mRNAs and acts as a molecular mediator between RNA polymerase II and U1 small nuclear ribonucleoprotein thereby coupling transcription and splicing. The 2 volumes review current knowledge and understanding, provide a starting point for researchers and practitioners entering the field, and build a platform for further research and discovery. This negative information provides a great pool of candidate RBPs for biologists to conduct future . Here, we use single-cell RNA sequencing (RNA-seq) to define a cellular taxonomy of the mouse bone marrow stroma and its perturbation by malignancy. This data set has been made accessible for exploration and analysis, to researchers and clinicians with limited bioinformatics experience, on our online portal Haemosphere: https://www.haemosphere.org. Here, a computational model, named seq-ImmuCC, was developed to predict the constitution of 10 immune cells from the RNA-Seq data of mouse tissues. Combine your sample analysis with our experience and expertise in murine immuno-oncology studies. Track Hubs. Densely interconnected transcriptional circuits control cell states in human hematopoiesis. 8600 Rockville Pike Epub 2016 Aug 4. Xie J, Lou Q, Zeng Y, Liang Y, Xie S, Xu Q, Yuan L, Wang J, Jiang L, Mou L, Lin D, Zhao M. Front Cell Dev Biol. RNA-Seq is a powerful quantitative tool to explore genome wide expression. 2016; 44:D917–D924. Asian J Androl. See this image and copyright information in PMC. -, Teng M., Love M.I., Davis C.A., Djebali S., Dobin A., Graveley B.R., Li S., Mason C.E., Olson S., Pervouchine D. et al. Single cell (or single nucleus) RNA sequencing (RNA-Seq) is a scalable approach to provide genome-wide expression profiles for thousands of cells. In order to make the tissue-specific gene calculations more robust, we only used tissues that had ≥2 biological replicates. (2008) and Zhang et al. doi: 10.1371/journal.pcbi.1009368. Biomed. Careers. Supplementary Note 1. Haemosphere also includes nine other publicly available high-quality data sets relevant to haematopoiesis. Crit Rev Eukaryot Gene Expr. 2011; 144:296–309. RNAcentral is a comprehensive database of non-coding RNA sequences that represents all types of ncRNA from a broad range of organisms. 2021 Jun 8;16(6):1629-1643. doi: 10.1016/j.stemcr.2021.04.010. Filters for individual RNA-seq data sets and TPM expression bins have also been developed. The first processing step in the maturation of mouse precursor rRNA involves cleavage at nucleotide ca. New data filters on GXD's search summaries. doi: 10.1093/nar/gkv1101. Identification and analysis of house-keeping and tissue-specific genes based on RNA-seq data sets across 15 mouse tissues. Specifically analyzed in our workflow were more than 6.6-TB sequences from 1,321 RNA-Seq libraries from various mouse tissues and cell lines. This site needs JavaScript to work properly. Epub 2021 May 10. 5 B ) showed that, when mean values for scRNA-seq data were assumed, there was a much better correlation with the single-tubule data than when median values were used. POSTAR3 is a comprehensive database for exploring POST-trAnscriptional Regulation based on high-throughput sequencing data from 7 species, including human, mouse, zebrafish, fly, worm, Arabidopsis, and yeast.POSTAR3 is developed as the updated version of CLIPdb, POSTAR, and POSTAR2, which provides the largest binding sites collection of RNA-binding proteins and their . This volume focuses on the use of system genetic methods and the use of murine models to study the role of gene variants and environmental factors on human health and disease—what is now often called personalized or precision health care. During haematopoiesis, haematopoietic stem cells differentiate into restricted potential progenitors before maturing into the many lineages required for oxygen transport, wound healing and immune response. Scientific Data, Volume 5, Article number: 180160 (2018) (1) Search gene expression in vascular single cells Currently most methods take manual strategies to annotate cell types after clustering the single-cell RNA-seq data. This release includes: Proteins: 210,703,648 Transcripts: 40,213,945 Organisms: -. Differential contribution to gene expression prediction of histone modifications at enhancers or promoters. Epub 2015 Oct 26. We next tested the effect of CellMatch on the performance of SingleR and CHETAH. GXD has developed new filters that take advantage of the genetic, functional, phenotypic and disease-related information in MGI. -, Seita J., Sahoo D., Rossi D.J., Bhattacharya D., Serwold T., Inlay M.A., Ehrlich L.I.R., Fathman J.W., Dill D.L., Weissman I.L.. Gene expression commons: An open platform for absolute gene expression profiling. Bagger FO, Sasivarevic D, Sohi SH, Laursen LG, Pundhir S, Sønderby CK, Winther O, Rapin N, Porse BT. Some candidate reference transcript-specific primers were designed. Exon scrambling is a phenomenon in which the exons of an mRNA transcript are spliced in an order inconsistent with that of the genome. This book, written by experienced geneticists, covers topics ranging from the natural history of the mouse species, its handling and reproduction in the laboratory, and its classical genetics and cytogenetics, to modern issues including the ... doi: 10.1084/jem.20202733. TissueEnrich defines tissue-specific genes using RNA-Seq data from the HPA, GTEx, and mouse ENCODE. Utilize genes unique to our panel for highly accurate detection of key immune cell signatures. The features of H-DBAS is as follows; Representative AS variants (RASVs) were identified from 8 data sets consist of 6 mammalian model organisms (human, mouse, rat, chimpanzee, macaque and dog . Comprised of 49 chapters, this volume begins with an overview of what can be learned from the genetic analysis of the lac repressor, followed by a discussion on the topography of the interaction the lac repressor, RNA polymerase, and ... 3.1 RNA-seq BAM files. Mouse RNA was collected from three individuals and in nine tissues: brain, colon, heart, kidney, liver, lung, skeletal muscle, spleen, and testes. 2021 Apr 12;9:653308. doi: 10.3389/fcell.2021.653308. Found insideThis e-book focuses on the latest developments in the areas of physiology, genomics, infection and immunity, host-pathogen interaction, pathogenesis, antimicrobial resistance and therapy, molecular epidemiology, applied and environmental ... This site needs JavaScript to work properly. RNA-Seq data not yet included in this search. Involved in splicing. 4 Slides GMX-RNA-NGS-HuWTA-4 GeoMx Mouse Whole Transcriptome Atlas Mouse RNA for Illumina Systems RNA Probe set that targets 21,000+ transcripts for mouse protein coding genes plus ERCC negative controls to profile the whole transcriptome. 2013; 29:569–574. subunits. To effectively integrate these data into GXD, we processed these files further to compute averaged quantile normalized TPM values per gene per biological replicate set. Identification of epididymis-specific transcripts in the mouse and rat by transcriptional profiling. Studies of the bone marrow stroma have defined individual populations in the stem cell niche regulating hematopoietic regeneration and capable of initiating leuke- mia. Although the number of RNA-Seq datasets deposited publicly has increased over the past few years, incomplete annotation of the associated metadata limits their potential use. We have updated Haemopedia, a database of gene-expression profiles from a broad spectrum of haematopoietic cells, to include RNA-seq gene-expression data from both mice and humans. Prioritizing and characterizing functionally relevant genes across human tissues. GXD collects and integrates the gene expression information in MGI. The datasets used in the tool are: HPA Dataset: RNA-Seq data across 35 human tissues (Uhlén et al. We have updated Haemopedia, a database of gene-expression profiles from a broad spectrum of haematopoietic cells, to include RNA-seq gene-expression data from both mice and humans. Found insideThis book serves to provide solid grounding in the fundamentals of stromal immunology, focusing on the biological aspects of their function in addition to highlighting key areas for the development of the field in the future. Multi-dimensional scaling (MDS) plots of the (A) Haemopedia mouse RNA-seq…, Multi-species plot. Front Genet. 2021 Jun 23;12:689406. doi: 10.3389/fgene.2021.689406. PLoS One. Retina following TNFɑ and the gamma secretase inhibitor RO4929097 (T+R) treatment. We consistently annotated the CLIP-seq data sets and RBPs, and developed a user-friendly interface for rapid navigation of the CLIP-seq data. Here, we use next-generation RNA sequencing (RNA-seq, for definitions of RNA-seq related terms, see supplemental data, available on the Blood Web site; see the Supplemental Materials link at the top of the online article) 18-23 to provide the first detailed analysis of the mouse platelet transcriptome. Stem Cell Reports. This dissertation, "Integrated Bioinformatics Analysis of Genetic, Expression and Interaction Data to Understand the Molecular Mechanisms of Alzheimer's Disease" by Yizhen, Jia, 賈亦真, was obtained from The University of Hong Kong ... Squares are coloured by row based. Boxplots were generated using plotly package (Carson Sievert (2018) plotly for R. Two candidate reference transcripts proposed for PBMCs were most suitable for normalization in comparison with commonly used reference genes. This volume provides an overview of RNA bioinformatics methodologies, including basic strategies to predict secondary and tertiary structures, and novel algorithms based on massive RNA sequencing. This data set includes single cell and nuclear transcriptomic profiles, assayed from human and mouse brain regions. GXD has been expanded to include RNA-Seq data. To facilitate GSEA analysis of RNA-Seq data, we now also provide CHIP files to convert human and mouse Ensembl IDs to HUGO gene symbols. HRT Atlas also offers the most stable and suitable tissue selective candidate reference transcripts for normalization of qPCR experiments. Housekeeping and Reference Transcript Atlas v1.0 workflow. Clipboard, Search History, and several other advanced features are temporarily unavailable. RNA expression per gene is reported as the number of reads aligning within gene bounds, scaled by sequencing depth. Herrera-Uribe J, Wiarda JE, Sivasankaran SK, Daharsh L, Liu H, Byrne KA, Smith TPL, Lunney JK, Loving CL, Tuggle CK. In a comprehensive cell type-specific analysis of the brain transcriptome, Cahoy et al. This volume is essential for anyone struggling with the cellular heterogeneity field, and it connects this new area with the latest advances in innovative techniques combined with practical advice from international experts. -, Bagger F.O., Sasivarevic D., Sohi S.H., Laursen L.G., Pundhir S., Sønderby C.K., Winther O., Rapin N., Porse B.T.. BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis. To gain an overview of transcriptome-wide cytosine methylation, we performed bisulfite sequencing (BS-seq) of RNA derived from mouse ESCs and from the adult mouse brain. Each dot represents a sample and they are coloured by lineage as shown in the key. We have . GXD has been expanded to include RNA-Seq data. Int. Zebrafish. Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA Sequencing. We provide a 3-week turnaround from . PLoS One. An integrated analysis of human myeloid cells identifies gaps in in vitro models of in vivo biology. The data sets have been imported from the EMBL-EBI's Expression Atlas. Found inside – Page iiThe proposed book will be a comprehensive overview of the current state of basic and translational research on PDE inhibitors written by internationally recognized experts. RNAcentral is the world's largest RNA secondary structure database. RNA-Seq datasets in SFMetaDB have various types of SF manipulation (Figure 1a --sjdbOverhang speci es the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database. The package reads BAM file(s) to obtain read coverage information in different genomic regions. 2016 Jan 4;44(D1):D917-24. We have integrated these data with the other types of expression data in GXD and with the genetic, functional, phenotypic and disease-related information in MGI and thus made them accessible to many new search capabilities. After downloading and identification of HK genes and transcripts using a specific algorithm, transcripts of genes with unknown pseudogenes were used to select suitable candidate reference transcripts. It is usual that RNA-seq data, due to its short length or low-quality sequencing, have difficulties in finding significant protein alignments. Found inside – Page 101For transcriptome data, the RNA-Seq data was derived from GEO with the ID GSE39619, and was used to quantify the expression levels of lincRNAs in mouse ESCs ... Mouse RNA-Seq data of Mortazavi et al. Elucidating the editome: bioinformatics approaches for RNA editing detection. This heatmap was generated from…, MeSH The Mouse Nervous System offers a wealth of new information for experienced anatomists who work on mice. The book serves as a valuable resource for researchers and graduate students in neuroscience. The database was generated by mining massive human and mouse RNA-seq data sets, including 11 281 and 507 high-quality RNA-seq samples from 52 human non-disease tissues/cells and 14 healthy tissues/cells of C57BL/6 wild type mouse, respectively. Bisulfite sequencing of nuclear and total poly(A) RNA in embryonic stem cells and mouse brain Bisulfite treatment, m5C calling, and controls. Epub 2021 Jan 14. -, Novershtern N., Subramanian A., Lawton L.N., Mak R.H., Haining W.N., McConkey M.E., Habib N., Yosef N., Chang C.Y., Shay T. et al. This set now comprises data for 2,373 targeted mutants, an increase of 1,261 mutants. ( A ) The…, Screenshot of the candidate reference transcript search result page. (. Unable to load your collection due to an error, Unable to load your delegates due to an error. This book details protocols on classical methods and very modern ex vivo mammalian developmental kidney model systems. Retina following light damage. eCollection 2021. 2012; 7:1–11. González-Ramírez M, Ballaré C, Mugianesi F, Beringer M, Santanach A, Blanco E, Di Croce L. PLoS Comput Biol. doi: 10.1093/nar/gky1076. The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute ().The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a . In this initial launch RetSeq allows exploration of photoreceptor cells from house mouse (Mus musculus) by visualizing relevant RNA-Seq and transcription factor (TF) ChIP-Seq. Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse. Run a gene search for SOX2, PECAM1 or ACE2; Browse the full list of samples The Mouse Transcriptome Project was an NIH-supported initiative that generated a free, public database of gene transcripts for many mouse tissues. Human GRCh38 Mouse mm10 Taavitsainen S, Engedal N, Cao S, Handle F, Erickson A, Prekovic S, Wetterskog D, Tolonen T, Vuorinen EM, Kiviaho A, Nätkin R, Häkkinen T, Devlies W, Henttinen S, Kaarijärvi R, Lahnalampi M, Kaljunen H, Nowakowska K, Syvälä H, Bläuer M, Cremaschi P, Claessens F, Visakorpi T, Tammela TLJ, Murtola T, Granberg KJ, Lamb AD, Ketola K, Mills IG, Attard G, Wang W, Nykter M, Urbanucci A. Nat Commun. This book provides an overview of the rapidly advancing field of long ncRNAs, describing the epigenetic and non-epigenetic mechanisms by which they regulate various biological functions in model systems, from yeast to mammals. As RNA-Seq becomes increasingly popular, hundreds of RNA-Seq datasets have . The 2018 issue has a list of about 180 such databases and updates to previously described databases. 2016 Jan 15;576(1 Pt 3):560-70. doi: 10.1016/j.gene.2015.11.003. H-DBAS is a unique database of alternative splicing (AS) based on H-InvDB. PMC © The Author(s) 2020. RNA-seq Characterization of Sex-Differences in Adipose Tissue of Obesity Affected Patients: Computational Analysis of Differentially Expressed Coding and Non-Coding RNAs. Nucleic Acids Res. , Hannenhalli S. PLoS Comput Biol Shiny package and encapsulated into docker image for deployment patterning! Hk genes local Blast was performed against a custom EST mouse database data sets to... From multiple studies and present them through a unified framework provides processed RNA-seq data for 187,946 publicly mouse! Specific primers and predicted modifiers of gene expression prediction of histone modifications enhancers! 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