run_metadata: 44015
This data as json
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| 44015 | SRR6211474 | SRX3320751 | SRS2626325 | 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 | Time course 10h24h mRNA | GSM2830047 | source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Embryo|time point:10h 24h | Time course 10h24h mRNA | Library strategy: Targeted amplification Embryos were injected with Cas9 and sgRNA at the 1 cell stage. post 1 2 3 4 6 8 10 and 24 hours 2 3 embryos were collected and RNA and/or DNA were extracted using TRIzol Reagent according to the manufacturer’s protocols. Bulk scar libraries were produced similarly to the bulk libraries for the scar probabilities. For each sample we calculated the percentage of unscarred RFP. We fit a negative exponential to this data assuming that the fraction of unscarred RFP at t=0 was one. Genome build: N/A Supplementary files format and content: List of scar sequences with CIGAR and cell barcode. | Full organism | Trizol extraction of RNA. CEL seq | strain/background:Zebrabow M|tissue:Whole body|developmental stage:Embryo|time point:10h 24h | GSM2830047 | GSM2830047: Time course 10h24h mRNA; Danio rerio; OTHER | GSM2830047 | 1 | Trizol extraction of RNA. CEL seq | GEO Accession:GSM2830047 | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | NextSeq 500 | SRP121343 | dyn_RNA_10h24h_S13_R2_001.fastq.gz dyn_RNA_10h24h_S13_R1_001.fastq.gz | fastq fastq | 1456176300.0 | 9707842.0 | GSM2830047 r1 | 0:100 1:50 | A:216943159;C:398650961;G:516656316;T:323899428;N:26436 | 100 | 50 | 216943159 | 398650961 | 516656316 | 323899428 | 26436 | SRX3320751 | SRS2626325 | SRA623333 | GEO | Max Delbrück Center | 2 | 3e-05 | 0.00111 | 0.0 | 0.0011 | 0.99995 | 1.0 | 0.75 | 100 | 50 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | other | unknown | sc | single_cell_plate | celseq | Germany | 2017-10-24 | Undetermined | Embryo | Trunk | Surface Structure |