run_metadata: 43986
This data as json
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| 43986 | SRR6811829 | SRX3768869 | SRS3023385 | SRP121343 | PRJNA415636 | Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars | GSE106121 | Other | A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes. | pubmed:29644996 | Larva F1 1 mRNA | GSM3032172 | source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva | Larva F1 1 mRNA | Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. | Full organism | Single cell dissociation. 10X Genomics Chromium | strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva | GSM3032172 | GSM3032172: Larva F1 1 mRNA; Danio rerio; RNA Seq | GSM3032172 | 1 | Single cell dissociation. 10X Genomics Chromium | GEO Accession:GSM3032172 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP121343 | F1_1_wt_R1.fastq.gz F1_1_wt_R2.fastq.gz | fastq fastq | 26685876072.0 | 215208678.0 | GSM3032172 r1 | 0:26 1:98 | A:7365353958;C:6068313931;G:6251004125;T:6996410946;N:4793112 | 26 | 98 | 7365353958 | 6068313931 | 6251004125 | 6996410946 | 4793112 | SRX3768869 | SRS3023385 | SRA623333 | GEO | Max Delbrück Center | 2 | 0.00255 | 0.93758 | 0.00046 | 0.08179 | 0.99515 | 0.82637 | 0.35368 | 0.46605 | 26 | 98 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2018-03-06 | Larval | Larval | Trunk | Surface Structure |