Turbine’s Post

Good food for thought by Kristóf Szalay on the predictive capabilites of transcriptomics for perturbation response! Have a read about the concept of RNA footprints and how to leverage it in systems biology empowered by machine learning

3ʹ mRNA-seq is an effective tool for measuring gene expression in an unbiased and quantitative manner. However, existing technologies are too laborious and expensive to be applied to large scale projects with numerous samples. Alithea Genomics has developed a novel, proprietary technology called bulk RNA barcoding and sequencing (BRB-seq), which enables the streamlined preparation of 3ʹ mRNA-seq libraries for hundreds of RNA samples in a single tube. The cornerstone of this technology is the use of BRB-seq oligos, which are synthetic DNA oligonucleotides. The combination of the BRB-seq kits with the VIAFLO 96 and VIAFLO 384 systems provides a convenient, efficient and reliable workflow for massively multiplexed RNA-seq experiments. To find out more, read the following article:

🔍 A Major Advancement in Spatial Transcriptomics Analysis: Spapros A new study published in Nature Methods introduces Spapros, a breakthrough tool that redefines how one approaches gene selection and probe design for spatial transcriptomics. Spatial transcriptomics is transforming our understanding of tissues by mapping gene expression with spatial context. However, selecting an optimal set of genes for these experiments—balancing cell type recovery and spatial variation—has been a major bottleneck. Spapros tackles this by: • Integrating probe design and gene selection in a single pipeline, saving time and reducing trial-and-error. • Optimizing for both cell type identification and spatial variation, allowing researchers to detect subtle, spatially-resolved biological patterns. • Performing exceptionally well across datasets, making it versatile and robust for diverse research needs. This study demonstrates Spapros’ ability to uncover fine-scale spatial variation even within cell types. This tool also expands the potential for spatial transcriptomics to answer complex biological questions, from tissue organization to disease mechanisms. #SpatialTranscriptomics #GeneSelection #Bioinformatics #TissueAnalysis

📃Scientific paper: K-Nearest-Neighbors Induced Topological PCA for scRNA Sequence Data Analysis Abstract: Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells, which has given us insights into cell-cell communication, cell differentiation, and differential gene expression. However, analyzing scRNA-seq data is a challenge due to sparsity and the large number of genes involved. Therefore, dimensionality reduction and feature selection are important for removing spurious signals and enhancing downstream analysis. Traditional PCA, a main workhorse in dimensionality reduction, lacks the ability to capture geometrical structure information embedded in the data, and previous graph Laplacian regularizations are limited by the analysis of only a single scale. We propose a topological Principal Components Analysis (tPCA) method by the combination of persistent Laplacian (PL) technique and L$_{2,1}$ norm regularization to address multiscale and multiclass heterogeneity issues in data. We further introduce a k-Nearest-Neighbor (kNN) persistent Laplacian technique to improve the robustness of our persistent Laplacian method. The proposed kNN-PL is a new algebraic topology technique which addresses the many limitations of the traditional persistent homology. Rather than inducing filtration via the varying of a distance threshold, we introduced kNN-tPCA, where filtrations are achieved by varying the number of neighbors in a kNN network at each step, and find that this framework has significant implications for hyper-parameter tuning. We validate the e... Continued on ES/IODE ➡️ https://etcse.fr/X9Ok ------- If you find this interesting, feel free to follow, comment and share. We need your help to enhance our visibility, so that our platform continues to serve you.

Unlock Deeper Biological Insights with Creative Proteomics' Integrated Transcriptomics and Metabolomics Analysis Service! At Creative Proteomics, we are proud to offer our advanced Integrated Transcriptomics and Metabolomics Analysis service. By combining the power of transcriptomics and metabolomics, we provide a comprehensive approach to understanding the complex molecular mechanisms underlying biological processes and diseases. Our service enables: Holistic analysis of gene function and structure Detailed examination of metabolomes to reflect physiological states Identification of key metabolic pathways and regulatory networks Enhanced understanding of cause-and-effect relationships in biological systems With our cutting-edge sequencing platform and extensive multi-omics co-analysis experience, we deliver high-quality data and insights that drive your research forward. Trust Creative Proteomics to support your next breakthrough in biological research. Discover more about our Integrated Transcriptomics and Metabolomics Analysis service: https://lnkd.in/gvHUhmNZ #Transcriptomics #Metabolomics #MultiOmics 

A multitude of different omics methods – including proteomics, transcriptomics, genomics, metabolomics, lipidomics and epigenomics – can be used to obtain a vast number of molecular measurements within a tissue or cell. But which omics approach will best empower your research? Here, we discuss the union of transcriptomics and proteomics and how using both of these methods can result in better, more reliable insight into the complex regulatory network of gene expression and gives you a bigger and better picture of what’s going on with your data: https://lnkd.in/gd53JFyr #scienceblog #multiomics #themoreyouknow

Single-cell transcriptomics is reshaping gene expression analysis as the cutting-edge RNA transcriptome tool! 🧬 Explore RNA Velocity, Trajectory analysis, and Spatial transcriptomics to delve deep into the dynamics of RNA. RNA Velocity captures immediate gene expression fluctuations within cells, while Trajectory analysis traces their long-term developmental paths. 🚀 🔍 Discover RNA Velocity Analysis: Uncover RNA Velocity with popular tools like #velocyto and #scVelo. Explore the integration of RNA velocity and gene regulatory dynamics in the trajectory analysis tool Dynamo, as highlighted in Cell. Don't miss the influential paper by La Manno et al., 2018 in Nature on RNA Velocity. Dive into the current landscape and future of RNA Velocity analysis with a 2021 paper by the developers of scVelo, Bergan and team. 🌱 Delve into Trajectory Analysis: Tools like #Monocle reconstruct cell differentiation processes, while #Scanpy’s PAGA and #Slingshot tool excel in pseudotime ordering and trajectory estimation using statistical frameworks. 🔬 Explore Spatial Transcriptomics Analysis: Discover the power of Spatial transcriptomics in mapping cell types and states within tissues with spatial information intact. This analysis offers a superior alternative to traditional in situ hybridization. Analyze with #Seurat and #Scanpy for comprehensive insights. Don't miss out on the future of gene expression analysis! 🌟 #Genomics #Bioinformatics #RNAVelocity #Trajectory #SingleCell #RNASeq #SpatialTranscriptomics #SnowflakeSquad Image reference of Spatial Transcriptomics Analysis from Junzhi Liu et al., 2024 for more insights: https://lnkd.in/gTz2fwMm

Transcription of DNA is a fundamental process in molecular biology where the genetic information encoded in DNA is converted into RNA. Here's a simplified explanation suitable for a class 12 level Examination - 𝐈𝐧𝐢𝐭𝐢𝐚𝐭𝐢𝐨𝐧 : Transcription begins with the binding of an enzyme called RNA polymerase to a specific region of DNA known as the promoter. The promoter signals the start of a gene, indicating to the RNA polymerase where to begin transcription. 𝐄𝐥𝐨𝐧𝐠𝐚𝐭𝐢𝐨𝐧 : Once RNA polymerase is bound to the promoter, it moves along the DNA strand, unwinding the double helix. As it progresses, it reads the DNA sequence and synthesizes a complementary RNA strand. The RNA strand is built one nucleotide at a time, with RNA polymerase adding nucleotides that are complementary to the DNA template strand. 𝐓𝐞𝐫𝐦𝐢𝐧𝐚𝐭𝐢𝐨𝐧 : Transcription continues until RNA polymerase reaches a specific sequence on the DNA called the terminator. At this point, RNA polymerase releases both the newly synthesized RNA strand and the DNA template. The RNA molecule, now called pre-mRNA, is released into the nucleus. 𝐏𝐫𝐨𝐜𝐞𝐬𝐬𝐢𝐧𝐠 : In eukaryotic cells, the pre-mRNA undergoes several modifications before it can serve as mature mRNA. These modifications include: Addition of a protective cap (5' cap) at the beginning of the mRNA molecule. Addition of a poly-A tail (polyadenylation) at the end of the mRNA molecule. Removal of non-coding regions called introns through a process called splicing. The remaining coding regions, called exons, are joined together to form the mature mRNA. 𝐄𝐱𝐩𝐨𝐫𝐭 : Once processed, the mature mRNA molecule is transported out of the nucleus and into the cytoplasm, where it serves as a template for protein synthesis during translation. Overall, transcription is a crucial step in the flow of genetic information from DNA to RNA, ultimately leading to the production of proteins that carry out various functions within the cell. . . . #TranscriptionProcessDNA #biology #12thbiology #CellBiology #Genetics #Evolution #StudentSupport #StudentMotivation #bcagurugram #basicconceptsacademy

🚨 Are you attending Single Cell Genomics 2024? 🚨 Come and meet us and learn about the latest advancements with Oxford Nanopore Technologies! Let’s talk about how nanopore sequencing delivers: *** Transcriptome & Epitranscriptome Analysis: Gain isoform-level insights with full-length transcript sequencing—direct RNA sequencing to detect modifications like m6A, without PCR bias. ***Single Cell Resolution: Full-length transcript analysis reveals cellular heterogeneity with comprehensive isoform diversity, splicing, and variant expression. Oxford Nanopore Technologies sequencing seamlessly integrates with Chromium Single Cell and Visium Spatial Gene Expression assays for single-cell workflows. Cell barcoding and UMI assignments can be resolved with our data alone! ***Haplotype-level Phasing: Long reads provide confident phasing, minimizing amplification bias and uncovering regions traditional methods miss. ***Genomic & Epigenomic Data: Directly analyze native DNA with no PCR required—capture SNVs, SVs, CNVs, and methylation data (5mC, 5hmC) in a single run. Come by for a chat! We are excited to discuss how you can elevate your single-cell research with nanopore technology. #SCG2024 #NanoporeSequencing #SingleCellGenomics #Genomics #Transcriptomics #Epigenomics #OxfordNanopore #SingleCell #Nanopore

Excited to share our latest work in which we profiled tRNA modifications using Nanopore direct RNA sequencing, combined with mass spectrometry and the facile genetics of the miracle organism, budding yeast. This was highly collaborative and synergistic effort, involving four institutions! First of all, tRNAs, where do I begin? They may be small, but they are oh-so mighty. Highly structured. Highly (chemically) modified. Abundant. Conserved. Interpreters of the genetic code. With few exceptions, every amino acid in every protein synthesized in every cell in every organism on earth, it was a tRNA that brought it there. Drop what you are doing and study them! That’s what we did. But, our scientific forebears, and so many contemporary labs, have done *so* much already. Documenting, seemingly, every last detail of them in so many contexts. What could we ever add? I think we added something. We are not the only ones, but we have been working incredibly hard to develop Nanopore direct RNA sequencing as an approach to survey tRNAs. Their sequences, their modifications, the interplay between modifications, and how environment influence them, too. The technique is particularly useful in its potential to profile multiple modifications simultaneously. It isn’t perfect, but some of its imperfections can be offset by rigorous application of control sequences, and more direct physical measurements from mass spectrometry, as we've done here. I hope that you enjoy it and if you are ever in the mood to sequence some tRNAs, from any organism or condition, do get in touch! https://lnkd.in/dMx8hXMb