Project description:In present study we optimized and validated the mDOT-seq approach with miRXplore Universal Reference (Miltenyi Biotec) RNA. The results revealed that the 3' adapters with alkyne moieties attached to the fifth carbon atom of the second cytosine or uracil in ACTC and CUCC sequences, respectively, are best suited for the preparation of RNA sequencing libraries.
Project description:We systematically benchmarked 8 single-cell ATAC sequencing technologies for their capacity to generate high-quality single-cell open chromatin profiles, and to elucidate the regulatory landscape of complex samples. Our study contains 47 individual human PBMC scATAC-seq experiments from a reference male and female donor. To streamline data analysis, we devised PUMATAC (https://github.com/aertslab/PUMATAC), a flexible and universal data analysis pipeline and best practices repository for scATAC-seq. Systematic technology-specific differences in sequencing library complexity and biases in tagmentation specificity were found to impact the accuracy of cell type annotation, genotype demultiplexing, peak calling, differential region accessibility, and motif enrichment. Together, our data forms a new scATAC-seq reference of more than 169, 000 PBMC cells with matched single-cell multiome and RNA-seq data.
Project description:Aging is a universal biological phenomenon linked to many diseases, such as cancer or neurodegeneration. However, the molecular mechanisms underlying aging, or how lifestyle interventions such as cognitive stimulation can ameliorate this process, are yet to be clarified. Here, we performed a multi-omic profiling, including RNA-seq, ATAC-seq, ChIP-seq, EM-seq, SWATH-MS and single cell Multiome scRNA and scATAC-seq, in the dorsal hippocampus of young and old mouse subjects which were subject to cognitive stimulation using the paradigm of environmental enrichment. In this study we were able to describe the epigenomic landscape of aging and cognitive stimulation.
2023-09-29 | PXD045567 | Pride
Project description:Improved TGIRT-seq methods for universal human reference RNA and miRXplore miRNA reference set
Project description:Prostate adenocarcinoma and matched adjacent normal samples were profiled by deep transcriptional sequencing to analyze transcription-induced chimeras and gene fusions. Reference samples from the MAQC and brain and universal reference libraries were also sequenced.
Project description:An updated representation of S. meliloti metabolism that was manually-curated and encompasses information from 240 literature sources, which includes transposon-sequencing (Tn-seq) data and Phenotype MicroArray data for wild-type and mutant strains.
Project description:We have developed two methods for efficiently consructing RNA-seq libraries using transposition. Each method constructs high quality RNA-seq libraries when compared to standard approaches. One of the methods (Directional Tn-RNA-seq) maintains strand-of-origin information and exhibits strand specificity comparable to current approaches. RNA-seq libraries were constructed from ECC-1, a human cell line, and Universal Human Reference RNA using transposon-based and standard RNA-seq library construciton methods.
Project description:We describe PolyA-Seq, a strand-specific method for high-throughput sequencing of the 3' ends of polyadenylated transcripts. PolyA-Seq is as accurate for digital gene expression as existing RNA sequencing approaches, and superior to microarrays. We used the approach to map polyadenylation (polyA) sites in 24 samples from normal tissues in human, rhesus, dog, mouse, and rat. Detection of polyA sites in a mixture of 24 tissues in human, mouse, rat, dog and rhesus. Samples included two replicates each of MAQC Human Brain Reference and MAQC Universal Human Reference. Two additional human sets of reads are included that were used to distinguish true polyA sites from internal priming sites.
Project description:Array hybridizations profiling diverse human tissues; for each array the human tissue RNA is hybridized against a universal reference RNA. Experiments 1-3 are replicates of universal reference RNA vs. genomic DNA hybridizations, used to estimate transcript abundance. Arrays 4-8 are tissue RNA vs. genomic DNA hybridizations, carried out to evaluate the method for estimating transcript abundance (see manuscript for details). Logical set Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: other