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Showing 1 to 14 of 14 for “"10X Genomics"”.
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Profiling the dynamics of the active transcriptome in the juvenile and adult brain using spatial transcriptomics
… the initial screening of the tissue samples. The 10x Genomics Visium Spatial gene expression system was used to obtain genome-wide spatial gene expression patterns. The Visium FASTQ files were aligned to the human transcriptome using 10X Genomics SpaceRanger. To spatially map the brain cell types, …
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Fast and accurate alignment of barcoded reads
… by instead producing "barcoded reads", including 10x Genomics' Chromium platform and Illumina's TruSeq Synthetic Long-Read platform. With barcoded reads, long-range information is captured by the barcodes, which identify source DNA fragments. As with all sequencing data, alignment of barcoded …
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Exploring the gene regulatory dynamics of the maturing human brain
… (snRNA-seq) libraries were generated using the 10x Genomics Platform. snRNA-seq datasets were then sequenced and analysed using bioinformatics tools, including Cell Ranger and Seurat. The major cell types in the pediatric brain were identified, including the genes being expressed by these cell …
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Towards a complete human cell atlas: a single-nucleus RNA sequencing study of the paediatric and adult human brain
… cortex origin and were produced using the 10X Genomics Single Cell 3' gene expression analysis kits. The datasets were processed using an optimised pipeline and the nuclei were annotated into various cell types using the Allen Institute's middle temporal gyrus dataset as a reference. A …
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The Evolution of Glioblastoma: A Single Case Study
… We performed linked-read sequencing using the 10X Genomics Chromium technology to reconstruct the DM and shed light on its emergence.
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Multi-Pronged Approach to Understanding the Toxicity Associated with CAR T-Cell Therapy
… and mononuclear cell enrichment, compatible with 10x Genomics platforms. Although the intended patient cohort study was not completed due to funding limitations, the established pipeline provides the means to study transcriptomic signatures of toxicity in future clinical material. I explored …
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Phenotypic and Functional Characterisation of Hofbauer Cells Across Gestation
… DR expression. Analysis of publicly available 10X Genomics single-cell RNA-sequencing data determined that full-term HBC heterogeneity was restricted to variable HLA-DR expression. Furthermore, a robust bulk RNA-sequencing dataset was generated to profile placental macrophages from the first …
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Enrichment and Transcriptome Analysis of CD4+ T Cell Clones Harboring Intact HIV-1 Proviruses
… cell gene expression and TCR sequencing on the 10x Genomics platform. Cells pertaining to expanded infected clones harboring an intact provirus are predominantly found in the CD4+ T effector memory compartment, but also belong to other CD4+ memory cell populations. Thus, expanded infected clones …
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Characterisation of Plasmodium parasite sexual commitment and development
… at high resolution. In this thesis, I use 10x Genomics single cell capture to sample the transcriptome of over 30,000 single cells from time points spanning the sexual developmental pathway of P. falciparum, from asexual growth, to sexual commitment, and into sexual maturity. I first use …
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Using single cell RNA sequencing to assess immunological responses in quails injected with porcine circovirus-like particles
… the transcriptome from the immunized quails, the 10X Genomics Chromium platform was used to isolate the PBMC samples into individual droplets, extract the mRNA from each cell, and synthesize barcoded cDNA that was then sequenced. Sequenced reads were analysed bioinformatically using software …
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Genetic characterization of Rpp1-mediated Asian soybean rust resistance using in-depth transcriptomic and genomic analyses
… were conducted on TMG06_0011 using the new 10X Genomics technology. Due to the lack of biological replications, the statistical analysis of differential expressed genes was computed by combining the results from GFOLD and EdgeR by using time points within a treatment as replicates. By …
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Single-cell genomics in rabbit and mouse elucidate eutherian embryonic development
… adaptable to deploy single-cell comparative genomics more broadly across biomedical research. Due to the genetic tractability of mouse, we aimed to interrogate the role key transcription factors (TFs) such as Zic2/3, Mix-like 1(Mixl1), Eomesodermin (Eomes), Stat3, and Runx1 in early …
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Resolving Cell Fate: Experimental, computational and mathematical methods in single cell transcriptomic analysis
Deeper understanding of the embryological origins of tissues and organs is likely to provide insights into novel clinically relevant preventative and therapeutic strategies. To do so effectively and at a large scale so as to have clinical significance requires an exhaustive and meticulously …
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CRISPR activation screening at single-cell transcriptomic resolution: discovering new regulators of zygotic genome activation
The maternal-to-zygotic transition in mammals consist of the passing of the developmental control from the mother to the embryo and involves two major events: the depletion of maternal products and the activation of the zygotic genome. Zygotic genome activation, or ZGA, coincides with dramatic …