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130 results for “Lineage tracing”
ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing data
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Data from: Whole organism lineage tracing by combinatorial and cumulative genome editing
Multicellular systems develop from single cells through distinct lineages. However, current lineage-tracing approaches scale poorly to whole, complex organisms. Here, we use genome editing to progressively introduce and accumulate diverse mutations in a DNA barcode over multiple rounds of cell division. The barcode, an array of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 target sites, marks cells and enables the elucidation of lineage relationships via the patterns of mutations shared between cells. In cell culture and zebrafish, we show that rates and patterns of editing are tunable and that thousands of lineage-informative barcode alleles can be generated. By sampling hundreds of thousands of cells from individual zebrafish, we find that most cells in adult organs derive from relatively few embryonic progenitors. In future analyses, genome editing of synthetic target arrays for lineage tracing (GESTALT) can be used to generate large-scale maps of cell lineage in multicellular systems for normal development and disease.
Systematic lineage tracing unveils polyclonal origin and evolution in colorectal precancer
<p>Data and code for <em><strong>Systematic lineage tracing unveils polyclonal origin and evolution in colorectal precancer</strong></em>: </p> <p>This dataset contains reproducibility, pipeline and data for 4 parts of the paper, including PacBio data analysis, scRNA-seq data analysis, HumanCRC data analysis and WGS data analysis. </p> <p>See <em>readme.txt</em> in each folder for more details. </p>
Data from: Whole organism lineage tracing by combinatorial and cumulative genome editing
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Inference of single-cell phylogenies from lineage tracing data with Cassiopeia
<p>Synthetic benchmarking data used in our study entitled "Inference of single-cell phylogenies from lineage tracing data with Cassiopeia" published in <em>Genome Biology</em>. </p> <p>Phylogenies were simulated with varying characters, states, experimental durations, mutation rates, dropout rates, and state distributions as described in our manuscript. This dataset includes simulated phylogenies of size 400 and 1000 cells. </p> <p>Each phylogeny is saved as a python Networkx object, pickled for convenience. These objects can be read in using Python version >= 3 with the "pickle" library. </p> <p>For stress testing and simulating additional phylogenies, please refer to our Github: https://github.com/YosefLab/Cassiopeia</p>
Data from: Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching
Antibody class switching is a feature of the adaptive immune system which enables diversification of the effector properties of antibodies. Even though class switching is essential for mounting a protective response to pathogens, the in vivo patterns and lineage characteristics of antibody class switching have remained uncharacterized in living humans. Here we comprehensively measured the landscape of antibody class switching in human adult twins using antibody repertoire sequencing. The map identifies how antibodies of every class are created and delineates a two-tiered hierarchy of class switch pathways. Using somatic hypermutations as a molecular clock, we discovered that closely related B cells often switch to the same class, but lose coherence as somatic mutations accumulate. Such correlations between closely related cells exist when purified B cells class switch in vitro, suggesting that class switch recombination is directed toward specific isotypes by a cell-autonomous imprinted state.
Data from: Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching
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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.
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.
Drosophila single-cell expression data of enteroendocrine cell lineage-traced guts, and guts under control and Xrp1 overexpression conditions in enteroendocrine cells.
GEO Series GSE301623. Drosophila melanogaster. 5 samples. Type: Expression profiling by high throughput sequencing.
Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection
GEO Series GSE134506. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Single-cell lineage tracing of ispinesib-resistant glioma cells
GEO Series GSE239651. Homo sapiens; Mus musculus. 90 samples. Type: Expression profiling by high throughput sequencing.
Systematic lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade [scRNA-seq]
GEO Series GSE185204. Homo sapiens. 40 samples. Type: Expression profiling by high throughput sequencing; Other.
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.
Lineage tracing reveals the pro-tumorigenic niche role of tissue resident macrophages in early lung cancer lesions I
GEO Series GSE147665. Mus musculus. 9 samples. Type: Expression 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.
Prospective identification and lineage tracing of top-level hematopoietic stem cells that sustain adult hematopoiesis
GEO Series GSE78855. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq-add]
GEO Series GSE277789. Mus musculus. 830 samples. Type: Expression profiling by high throughput sequencing.
Human lineage tracing enabled by mitochondrial mutations and single cell genomics [CC100_scATAC]
GEO Series GSE115216. Homo sapiens. 192 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Endothelial plasticity in atrial fibrosis by integrating single-cell sequencing and genetic lineage tracing
GEO Series GSE198204. Homo sapiens; Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.