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371
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ShareScore release 0.9.0
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371 results for “single cell genomics”
Genome sequencing of P. tricornutum mother and daughter cultures derived from single cell and separated by 30 days of proliferation - processed datasets
<p><strong>Genome sequencing of <em>P. tricornutum</em> mother and daughter cultures derived from single cell and separated by 30 days of proliferation - processed datasets.</strong></p> <p>Raw data for this experiment are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA658224.</p> <p> </p> <p><strong>Please note that the naming of files differs from the general description on /www.ncbi.nlm.nih.gov/bioproject website and in related publication:</strong></p> <p>Instead of MC1-3, the processed datasets are labelled Sc1-3</p> <p>Instead of DC1.1; DC1.2 and DC1.3, the processed datasets are labelled Sc11, Sc12 and Sc14 respectively</p> <p>Instead of DC2.1; DC2.2 and DC2.3, the processed datasets are labelled Sc21, Sc22 and Sc24 respectively</p> <p>Instead of DC3.1; DC3.2 and DC3.3, the processed datasets are labelled Sc31, Sc32 and Sc33 respectively</p> <p><strong>Available datasets: </strong></p> <p><em>.bam</em> files with ILLUMINA reads aligned to the reference P. tricornutum v2 genome used for SNP calling </p> <p><em>.vcf</em> files for individual samples with SNPs called using GATK3.7.0</p> <p><em>joint_genotyping_cohort.vcf</em> file with SNPs called jointly for all samples using GATK4.2.1 </p> <p> </p> <p><strong>Description of the experiment:</strong> </p> <p>Whole-genome Illumina sequencing of mother and daughter cultures derived from single cell to reveal genomic changes occurring within 30 day time frame. Three independent single cells were isolated from CCAP 1055/1 culture (sample label: Pt1) to start mother cultures (MC1; MC2; MC3 . On day 30 after mother culture isolation (T1 time point), three daughter cells were isolated from each mother culture forming cultures DC11-DC33. Part of mother cultures and CCAP 1055/1 culture were harvested at T1 (Samples: Pt1T1; MC1T1; MC2T1; MC3T1) . After another 30 days (T2 time point), all cultures were harvested (Samples: Pt1T2; mother culture MC1T2 and respective daughter cultures DC11, DC12 and DC13 ; mother culture MC2T2 and respective daughter cultures DC21, DC22 and DC23; mother culture MC3T1 and respective daughter cultures DC31, DC32, DC33).</p>
Data from: Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus
Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct "genomic backbones," each backbone consisting of a different set of core gene alleles linked to a small distinctive set of flexible genes. These subpopulations are estimated to have diverged at least a few million years ago, suggesting ancient, stable niche partitioning. Such a large set of coexisting subpopulations may be a general feature of free-living bacterial species with huge populations in highly mixed habitats.
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)
<p><strong>Datasets for PILOT</strong></p> <p>Although clinical applications represent the next challenge in single-cell genomics and digital pathology, we are still lacking computational methods for the analysis of single-cell and pathomics data at a patient level for finding patient trajectories associated with diseases. This is challenging as a single-cell/pathomics data is represented by clusters of cells/structures, which cannot be compared with other samples. We propose here patient Level analysis with Optimal Transport (PILOT). PILOT uses optimal transport to compute the Wasserstein distance between two single single-cell experiments. This allows us to perform unsupervised analysis at the sample level and to uncover trajectories associated with disease progression. Moreover, PILOT provides a statistical approach to delineate non-linear changes in cell populations, gene expression and tissues structures related to the disease trajectories. We evaluate PILOT and competing approaches in disease single-cell genomics and pathomics studies with up to 1.000 patients/donors and millions of cells or structures. Results demonstrate that PILOT detects disease-associated samples, cells, and genes from large and complex single-cell and pathomics data.</p>
Healthy woodchuck genome with viral sequences appended used for single-cell RNA-seq analysis
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Genomic and single-cell characterization of patient-derived tumor organoid models of head and neck squamous cell carcinoma
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Data from: Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus
Open the record for dataset details and reuse information.
Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics [10X_scRNAseq]
GEO Series GSE141589. Drosophila melanogaster. 1 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide profiling of DNA repair proteins in single cells
GEO Series GSE229874. Homo sapiens. 55 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing.
Multiplex generation and single cell analysis of structural variants in mammalian genomes [scRNA-seq]
GEO Series GSE282634. Homo sapiens; Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing; Other.
Human lineage tracing enabled by mitochondrial mutations and single cell genomics [Colonies_scRNA]
GEO Series GSE115214. Homo sapiens. 1016 samples. Type: Expression profiling by high throughput sequencing.
10X Genomics single-cell RNA-Seq data set of CreER mice
GEO Series GSE162713. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Single-cell RNAseq analysis (10X Genomics Chromium) of cMAF- and Mafb-deficent lung monocytes and interstium macrophages
GEO Series GSE193891. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Human lineage tracing enabled by mitochondrial mutations and single cell genomics [TF1_clones_ATAC]
GEO Series GSE115208. Homo sapiens. 69 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A single-cell transcriptomics CRISPR-activation screen identifies new epigenetic regulators of the zygotic genome activation programm (10X Genomics CRISPRa screen dataset)
GEO Series GSE135621. Mus musculus. 27 samples. Type: Expression profiling by high throughput sequencing.
CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics
GEO Series GSE130065. Mus musculus; Homo sapiens. 5 samples. Type: Expression profiling by high throughput sequencing.
Human lineage tracing enabled by mitochondrial mutations and single cell genomics
GEO Series GSE115218. Homo sapiens. 2733 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other.
Genome-wide profiling at single-nucleotide resolution of brain cell types in schizophrenia [WGBS]
GEO Series GSE107729. Homo sapiens. 95 samples. Type: Methylation profiling by high throughput sequencing.
Human lineage tracing enabled by mitochondrial mutations and single cell genomics [TF1_barcoding_scRNA]
GEO Series GSE118203. Homo sapiens. 384 samples. Type: Expression profiling by high throughput sequencing.
DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells
GEO Series GSE128560. Homo sapiens. 29 samples. Type: Methylation profiling by high throughput sequencing.
Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells
GEO Series GSE75346. Homo sapiens. 65 samples. Type: Methylation profiling by high throughput sequencing.
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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.
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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.